

     ______  ____   ____  ____   ____  ______  __ __
    |      ||    \ |    ||    \ |    ||      ||  |  |
    |      ||  D  ) |  | |  _  | |  | |      ||  |  |
    |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
      |  |  |    \  |  | |  |  | |  |   |  |  |___, |
      |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
      |__|  |__|\_||____||__|__||____|  |__|  |____/

    Trinity-v2.15.1



Left read files: $VAR1 = [
          '/outputs/TEDreads_fqs/SRR12904817_R1_ted_mtx.fastq.gz'
        ];
Right read files: $VAR1 = [
          '/outputs/TEDreads_fqs/SRR12904817_R2_ted_mtx.fastq.gz'
        ];
Trinity version: Trinity-v2.15.1
** NOTE: Latest version of Trinity is Trinity-v2.15.2, and can be obtained at:
	https://github.com/trinityrnaseq/trinityrnaseq/releases

Thursday, July 16, 2026: 20:13:01	CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /opt/conda/opt/trinity-2.15.1/util/support_scripts/ExitTester.jar 0
Thursday, July 16, 2026: 20:13:01	CMD: java -Xmx4g -XX:ParallelGCThreads=2  -jar /opt/conda/opt/trinity-2.15.1/util/support_scripts/ExitTester.jar 1
Thursday, July 16, 2026: 20:13:01	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817
Thursday, July 16, 2026: 20:13:01	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis


----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
----------------------------------------------------------------------------------

---------------------------------------------------------------
------------ In silico Read Normalization ---------------------
-- (Removing Excess Reads Beyond 200 Coverage --
---------------------------------------------------------------

# running normalization on reads: $VAR1 = [
          [
            '/outputs/TEDreads_fqs/SRR12904817_R1_ted_mtx.fastq.gz'
          ],
          [
            '/outputs/TEDreads_fqs/SRR12904817_R2_ted_mtx.fastq.gz'
          ]
        ];


Thursday, July 16, 2026: 20:13:01	CMD: /opt/conda/opt/trinity-2.15.1/util/insilico_read_normalization.pl --seqType fq --JM 62G  --max_cov 200 --min_cov 1 --CPU 12 --output /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/insilico_read_normalization --max_CV 10000  --left /outputs/TEDreads_fqs/SRR12904817_R1_ted_mtx.fastq.gz --right /outputs/TEDreads_fqs/SRR12904817_R2_ted_mtx.fastq.gz --pairs_together  --PARALLEL_STATS  
-prepping seqs
Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /outputs/TEDreads_fqs/SRR12904817_R1_ted_mtx.fastq.gz) >> left.fa
CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /outputs/TEDreads_fqs/SRR12904817_R2_ted_mtx.fastq.gz) >> right.fa
CMD finished (1 seconds)
CMD finished (1 seconds)
CMD: touch left.fa.ok
CMD finished (0 seconds)
CMD: touch right.fa.ok
CMD finished (0 seconds)
Done converting input files.CMD: cat left.fa right.fa > both.fa
CMD finished (0 seconds)
CMD: touch both.fa.ok
CMD finished (0 seconds)
-kmer counting.
-------------------------------------------
----------- Jellyfish  --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

CMD: jellyfish count -t 12 -m 25 -s 100000000  --canonical  both.fa
CMD finished (0 seconds)
CMD: jellyfish histo -t 12 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
CMD finished (1 seconds)
CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
CMD finished (0 seconds)
CMD: touch jellyfish.K25.min2.kmers.fa.success
CMD finished (0 seconds)
-generating stats files
CMD: /opt/conda/opt/trinity-2.15.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 6  --DS  > left.fa.K25.stats
-reading Kmer occurrences...
CMD: /opt/conda/opt/trinity-2.15.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 6  --DS  > right.fa.K25.stats
-reading Kmer occurrences...

 done parsing 2130265 Kmers, 2130265 added, taking 3 seconds.

 done parsing 2130265 Kmers, 2130265 added, taking 3 seconds.
STATS_GENERATION_TIME: 0 seconds.
STATS_GENERATION_TIME: 0 seconds.
CMD finished (4 seconds)
CMD finished (4 seconds)
CMD: touch left.fa.K25.stats.ok
CMD finished (0 seconds)
CMD: touch right.fa.K25.stats.ok
CMD finished (0 seconds)
-sorting each stats file by read name.
CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=12 -k1,1 -T . -S 31G >> left.fa.K25.stats.sort
CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=12 -k1,1 -T . -S 31G >> right.fa.K25.stats.sort
CMD finished (0 seconds)
CMD finished (0 seconds)
CMD: touch left.fa.K25.stats.sort.ok
CMD finished (0 seconds)
CMD: touch right.fa.K25.stats.sort.ok
CMD finished (0 seconds)
-defining normalized reads
CMD: /opt/conda/opt/trinity-2.15.1/util/..//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
-opening left.fa.K25.stats.sort
-opening right.fa.K25.stats.sort
-done opening files.
CMD finished (1 seconds)
CMD: touch pairs.K25.stats.ok
CMD finished (0 seconds)
CMD: /opt/conda/opt/trinity-2.15.1/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
55983 / 57124 = 98.00% reads selected during normalization.
0 / 57124 = 0.00% reads discarded as likely aberrant based on coverage profiles.
0 / 57124 = 0.00% reads discarded as below minimum coverage threshold=1
CMD finished (0 seconds)
CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
CMD finished (0 seconds)
-search and capture.
-preparing to extract selected reads from: /outputs/TEDreads_fqs/SRR12904817_R1_ted_mtx.fastq.gz ... done prepping, now search and capture.
-capturing normalized reads from: /outputs/TEDreads_fqs/SRR12904817_R1_ted_mtx.fastq.gz
-preparing to extract selected reads from: /outputs/TEDreads_fqs/SRR12904817_R2_ted_mtx.fastq.gz ... done prepping, now search and capture.
-capturing normalized reads from: /outputs/TEDreads_fqs/SRR12904817_R2_ted_mtx.fastq.gz
CMD: touch /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/insilico_read_normalization/SRR12904817_R1_ted_mtx.fastq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
CMD finished (0 seconds)
CMD: touch /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/insilico_read_normalization/SRR12904817_R2_ted_mtx.fastq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
CMD finished (0 seconds)
CMD: ln -sf /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/insilico_read_normalization/SRR12904817_R1_ted_mtx.fastq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
CMD finished (0 seconds)
CMD: ln -sf /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/insilico_read_normalization/SRR12904817_R2_ted_mtx.fastq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
CMD finished (0 seconds)
-removing tmp dir /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/insilico_read_normalization/tmp_normalized_reads


Normalization complete. See outputs: 
	/outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/insilico_read_normalization/SRR12904817_R1_ted_mtx.fastq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
	/outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/insilico_read_normalization/SRR12904817_R2_ted_mtx.fastq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
Thursday, July 16, 2026: 20:13:10	CMD: touch /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/insilico_read_normalization/normalization.ok
Converting input files. (in parallel)Thursday, July 16, 2026: 20:13:10	CMD: cat /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A -R 1 - >> left.fa
Thursday, July 16, 2026: 20:13:10	CMD: cat /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
Thursday, July 16, 2026: 20:13:10	CMD: touch left.fa.ok
Thursday, July 16, 2026: 20:13:10	CMD: touch right.fa.ok
Thursday, July 16, 2026: 20:13:10	CMD: touch left.fa.ok right.fa.ok
Thursday, July 16, 2026: 20:13:10	CMD: cat left.fa right.fa > /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/both.fa
Thursday, July 16, 2026: 20:13:10	CMD: touch /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/both.fa.ok
-------------------------------------------
----------- Jellyfish  --------------------
-- (building a k-mer (25) catalog from reads) --
-------------------------------------------

* [Thu Jul 16 20:13:10 2026] Running CMD: jellyfish count -t 12 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/both.fa
* [Thu Jul 16 20:13:11 2026] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
* [Thu Jul 16 20:13:11 2026] Running CMD: jellyfish histo -t 12 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
----------------------------------------------
--------------- Inchworm (K=25, asm) ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------

* [Thu Jul 16 20:13:12 2026] Running CMD: /opt/conda/opt/trinity-2.15.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --DS  --num_threads 6  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/inchworm.DS.fa.tmp
Kmer length set to: 25
Min assembly length set to: 25
Monitor turned on, set to: 1
double stranded mode set
min entropy set to: 1
setting number of threads to: 6
-setting parallel iworm mode.
-reading Kmer occurrences...

 [0M] Kmers parsed.     
 [1M] Kmers parsed.     
 [1M] Kmers parsed.     
 [2M] Kmers parsed.     
 [3M] Kmers parsed.     
 done parsing 3551343 Kmers, 3551343 added, taking 4 seconds.

TIMING KMER_DB_BUILDING 4 s.
Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
Pruned 750 kmers from catalog.
	Pruning time: 1 seconds = 0.0166667 minutes.

TIMING PRUNING 1 s.
-populating the kmer seed candidate list.
Kcounter hash size: 3551343
Processed 3550593 non-zero abundance kmers in kcounter.
-Not sorting list of kmers, given parallel mode in effect.
-beginning inchworm contig assembly.
Total kcounter hash size: 3551343 vs. sorted list size: 3550593
num threads set to: 6
Done opening file. tmp.iworm.fa.pid_1300.thread_0
Done opening file. tmp.iworm.fa.pid_1300.thread_1
Done opening file. tmp.iworm.fa.pid_1300.thread_2
Done opening file. tmp.iworm.fa.pid_1300.thread_3
Done opening file. tmp.iworm.fa.pid_1300.thread_4
Done opening file. tmp.iworm.fa.pid_1300.thread_5

	Iworm contig assembly time: 3 seconds = 0.05 minutes.

TIMING CONTIG_BUILDING 3 s.

TIMING PROG_RUNTIME 9 s.
* [Thu Jul 16 20:13:22 2026] Running CMD: mv /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/inchworm.DS.fa.tmp /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/inchworm.DS.fa
Thursday, July 16, 2026: 20:13:22	CMD: touch /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/inchworm.DS.fa.finished
--------------------------------------------------------
-------------------- Chrysalis -------------------------
-- (Contig Clustering & de Bruijn Graph Construction) --
--------------------------------------------------------

inchworm_target: /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/both.fa
bowtie_reads_fa: /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/both.fa
chrysalis_reads_fa: /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/both.fa
* [Thu Jul 16 20:13:22 2026] Running CMD: /opt/conda/opt/trinity-2.15.1/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/inchworm.DS.fa 100 10 > /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/inchworm.DS.fa.min100
* [Thu Jul 16 20:13:22 2026] Running CMD: /opt/conda/bin/bowtie2-build --threads 12 -o 3 /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/inchworm.DS.fa.min100 /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/inchworm.DS.fa.min100 1>/dev/null
* [Thu Jul 16 20:13:24 2026] Running CMD: bash -c " set -o pipefail;/opt/conda/bin/bowtie2 --local -k 2 --no-unal --threads 12 -f --score-min G,20,8 -x /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/inchworm.DS.fa.min100 /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/both.fa  | samtools view -@ 12 -F4 -Sb - | samtools sort -m 2773833045 -@ 12 -no /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/iworm.bowtie.nameSorted.bam" 
* [Thu Jul 16 20:13:26 2026] Running CMD: /opt/conda/opt/trinity-2.15.1/util/support_scripts/scaffold_iworm_contigs.pl /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/iworm.bowtie.nameSorted.bam /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/inchworm.DS.fa.min100 > /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/iworm_scaffolds.txt
* [Thu Jul 16 20:13:27 2026] Running CMD: /opt/conda/opt/trinity-2.15.1/Chrysalis/bin/GraphFromFasta -i /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/inchworm.DS.fa.min100 -r /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 12 -k 24 -kk 48  -scaffolding /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/iworm_scaffolds.txt  > /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/iworm_cluster_welds_graph.txt
* [Thu Jul 16 20:13:31 2026] Running CMD: /usr/bin/sort --parallel=12 -T . -S 62G  -k9,9gr /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/iworm_cluster_welds_graph.txt > /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/iworm_cluster_welds_graph.txt.sorted
* [Thu Jul 16 20:13:31 2026] Running CMD: /opt/conda/opt/trinity-2.15.1/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/inchworm.DS.fa.min100 /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/iworm_cluster_welds_graph.txt.sorted > /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
* [Thu Jul 16 20:13:32 2026] Running CMD: /opt/conda/opt/trinity-2.15.1/Chrysalis/bin/BubbleUpClustering -i /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/inchworm.DS.fa.min100  -weld_graph /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/GraphFromIwormFasta.out
* [Thu Jul 16 20:13:32 2026] Running CMD: /opt/conda/opt/trinity-2.15.1/Chrysalis/bin/CreateIwormFastaBundle -i /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/GraphFromIwormFasta.out -o /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/bundled_iworm_contigs.fasta -min 200
* [Thu Jul 16 20:13:32 2026] Running CMD: /opt/conda/opt/trinity-2.15.1/Chrysalis/bin/ReadsToTranscripts -i /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/both.fa -f /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/bundled_iworm_contigs.fasta -o /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/readsToComponents.out -t 12 -max_mem_reads 50000000  -p 10 
* [Thu Jul 16 20:13:41 2026] Running CMD: /usr/bin/sort --parallel=12 -T . -S 62G -k 1,1n -k3,3nr -k2,2 /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/readsToComponents.out > /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/chrysalis/readsToComponents.out.sort
Thursday, July 16, 2026: 20:13:41	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_0
Thursday, July 16, 2026: 20:13:41	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_1
Thursday, July 16, 2026: 20:13:41	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_2
Thursday, July 16, 2026: 20:13:42	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_3
Thursday, July 16, 2026: 20:13:42	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_4
Thursday, July 16, 2026: 20:13:42	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_5
Thursday, July 16, 2026: 20:13:42	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_6
Thursday, July 16, 2026: 20:13:42	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_7
Thursday, July 16, 2026: 20:13:43	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_8
Thursday, July 16, 2026: 20:13:43	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_9
Thursday, July 16, 2026: 20:13:43	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_10
Thursday, July 16, 2026: 20:13:43	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_11
Thursday, July 16, 2026: 20:13:43	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_12
Thursday, July 16, 2026: 20:13:43	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_13
Thursday, July 16, 2026: 20:13:44	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_14
Thursday, July 16, 2026: 20:13:44	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_15
Thursday, July 16, 2026: 20:13:44	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_16
Thursday, July 16, 2026: 20:13:44	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_17
Thursday, July 16, 2026: 20:13:44	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_18
Thursday, July 16, 2026: 20:13:44	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_19
Thursday, July 16, 2026: 20:13:44	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_20
Thursday, July 16, 2026: 20:13:45	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_21
Thursday, July 16, 2026: 20:13:45	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_22
Thursday, July 16, 2026: 20:13:45	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_23
Thursday, July 16, 2026: 20:13:45	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_24
Thursday, July 16, 2026: 20:13:45	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_25
Thursday, July 16, 2026: 20:13:45	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_26
Thursday, July 16, 2026: 20:13:45	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_27
Thursday, July 16, 2026: 20:13:46	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_28
Thursday, July 16, 2026: 20:13:46	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_29
Thursday, July 16, 2026: 20:13:46	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_30
Thursday, July 16, 2026: 20:13:46	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_31
Thursday, July 16, 2026: 20:13:46	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_32
Thursday, July 16, 2026: 20:13:46	CMD: mkdir -p /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/Fb_0/CBin_33
Thursday, July 16, 2026: 20:13:46	CMD: touch /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/partitioned_reads.files.list.ok
Thursday, July 16, 2026: 20:13:46	CMD: /opt/conda/opt/trinity-2.15.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --seqType fa --trinity_complete --full_cleanup  --bflyHeapSpaceMax  20G  --bflyCPU  2  --no_salmon  > recursive_trinity.cmds
Thursday, July 16, 2026: 20:13:46	CMD: touch recursive_trinity.cmds.ok
Thursday, July 16, 2026: 20:13:46	CMD: touch recursive_trinity.cmds.ok


--------------------------------------------------------------------------------
------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
--------------------------------------------------------------------------------

Thursday, July 16, 2026: 20:13:46	CMD: /opt/conda/opt/trinity-2.15.1/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 12 -v -shuffle 
Number of Commands: 3305

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All commands completed successfully. :-)



** Harvesting all assembled transcripts into a single multi-fasta file...

Thursday, July 16, 2026: 20:26:42	CMD: find /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/read_partitions/ -name '*inity.fasta'  | /opt/conda/opt/trinity-2.15.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/Trinity.tmp
* [Thu Jul 16 20:26:43 2026] Running CMD: /opt/conda/opt/trinity-2.15.1/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/both.fa 12
* [Thu Jul 16 20:26:44 2026] Running CMD: /opt/conda/opt/trinity-2.15.1/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817/both.fa salmon_outdir/quant.sf 2 > /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817.Trinity.fasta


#############################################################################
Finished.  Final Trinity assemblies are written to /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817.Trinity.fasta
#############################################################################


Thursday, July 16, 2026: 20:26:45	CMD: /opt/conda/opt/trinity-2.15.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817.Trinity.fasta > /outputs/asmbMTX/SRR12904817_asmb/trinity_SRR12904817.Trinity.fasta.gene_trans_map
