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BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
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bracer test failed on Recombinant-derived reads with Biopython errors #22

Closed JohnMCMa closed 6 years ago

JohnMCMa commented 6 years ago

I'm using RHEL with Python 3.6.1, biopython 1.70, igBLAST 1.9, blast 2.2.31, trinity 2.6.6. The software was installed with git as my system does not allow Docker.

I issued bracer test -p 4 -c ./Green/CommonCode/bracer.conf -o ./bracer_test/ > bracer-out.txt 2>&1 and the output are as follows:

56438 reads; of these:
  56438 (100.00%) were paired; of these:
    35350 (62.64%) aligned concordantly 0 times
    21088 (37.36%) aligned concordantly exactly 1 time
    0 (0.00%) aligned concordantly >1 times
    ----
    35350 pairs aligned concordantly 0 times; of these:
      73 (0.21%) aligned discordantly 1 time
    ----
    35277 pairs aligned 0 times concordantly or discordantly; of these:
      70554 mates make up the pairs; of these:
        69268 (98.18%) aligned 0 times
        232 (0.33%) aligned exactly 1 time
        1054 (1.49%) aligned >1 times
38.63% overall alignment rate
56438 reads; of these:
  56438 (100.00%) were paired; of these:
    56438 (100.00%) aligned concordantly 0 times
    0 (0.00%) aligned concordantly exactly 1 time
    0 (0.00%) aligned concordantly >1 times
    ----
    56438 pairs aligned concordantly 0 times; of these:
      0 (0.00%) aligned discordantly 1 time
    ----
    56438 pairs aligned 0 times concordantly or discordantly; of these:
      112876 mates make up the pairs; of these:
        112876 (100.00%) aligned 0 times
        0 (0.00%) aligned exactly 1 time
        0 (0.00%) aligned >1 times
0.00% overall alignment rate
56438 reads; of these:
  56438 (100.00%) were paired; of these:
    48319 (85.61%) aligned concordantly 0 times
    8119 (14.39%) aligned concordantly exactly 1 time
    0 (0.00%) aligned concordantly >1 times
    ----
    48319 pairs aligned concordantly 0 times; of these:
      114 (0.24%) aligned discordantly 1 time
    ----
    48205 pairs aligned 0 times concordantly or discordantly; of these:
      96410 mates make up the pairs; of these:
        95663 (99.23%) aligned 0 times
        195 (0.20%) aligned exactly 1 time
        552 (0.57%) aligned >1 times
15.25% overall alignment rate
56438 reads; of these:
  56438 (100.00%) were paired; of these:
    31766 (56.28%) aligned concordantly 0 times
    24672 (43.72%) aligned concordantly exactly 1 time
    0 (0.00%) aligned concordantly >1 times
    ----
    31766 pairs aligned concordantly 0 times; of these:
      270 (0.85%) aligned discordantly 1 time
    ----
    31496 pairs aligned 0 times concordantly or discordantly; of these:
      62992 mates make up the pairs; of these:
        61549 (97.71%) aligned 0 times
        144 (0.23%) aligned exactly 1 time
        1299 (2.06%) aligned >1 times
45.47% overall alignment rate

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

Left read files: $VAR1 = [
          '/scratch/lym_myl_rsch/mma/bracer_test/results/cell1/aligned_reads/cell1_BCR_H_1.fastq'
        ];
Right read files: $VAR1 = [
          '/scratch/lym_myl_rsch/mma/bracer_test/results/cell1/aligned_reads/cell1_BCR_H_2.fastq'
        ];
Trinity version: Trinity-v2.6.6
-ERROR: couldn't run the network check to confirm latest Trinity software version.

Tuesday, August 14, 2018: 11:20:01  CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /risapps/noarch/trinity/2.6.6/util/support_scripts/ExitTester.jar 0
Tuesday, August 14, 2018: 11:20:02  CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /risapps/noarch/trinity/2.6.6/util/support_scripts/ExitTester.jar 1
Tuesday, August 14, 2018: 11:20:02  CMD: mkdir -p /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_H
Tuesday, August 14, 2018: 11:20:02  CMD: mkdir -p /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_H/chrysalis

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

Converting input files. (in parallel)Tuesday, August 14, 2018: 11:20:02 CMD: cat /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/aligned_reads/cell1_BCR_H_1.fastq | seqtk-trinity seq -A - >> left.fa
Tuesday, August 14, 2018: 11:20:02  CMD: touch left.fa.ok
Tuesday, August 14, 2018: 11:20:02  CMD: cat /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/aligned_reads/cell1_BCR_H_2.fastq | seqtk-trinity seq -A - >> right.fa
Tuesday, August 14, 2018: 11:20:02  CMD: touch right.fa.ok
Tuesday, August 14, 2018: 11:20:02  CMD: touch left.fa.ok right.fa.ok
Tuesday, August 14, 2018: 11:20:02  CMD: cat left.fa right.fa > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_H/both.fa
Tuesday, August 14, 2018: 11:20:02  CMD: touch /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_H/both.fa.ok
-------------------------------------------
----------- Jellyfish  --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

* Running CMD: jellyfish count -t 4 -m 25 -s 100000000  --canonical  /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_H/both.fa
* Running CMD: jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa
* Running CMD: jellyfish histo -t 4 -o jellyfish.kmers.fa.histo mer_counts.jf
----------------------------------------------
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------

* Running CMD: /risapps/noarch/trinity/2.6.6/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1   --DS  --num_threads 4  --PARALLEL_IWORM  > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_H/inchworm.K25.L25.DS.fa.tmp
* Running CMD: mv /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_H/inchworm.K25.L25.DS.fa.tmp /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_H/inchworm.K25.L25.DS.fa
Tuesday, August 14, 2018: 11:20:03  CMD: touch /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_H/inchworm.K25.L25.DS.fa.finished
NON_FATAL_EXCEPTION: WARNING, no Inchworm output is detected at: /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_H/inchworm.K25.L25.DS.fa at /risapps/noarch/trinity/2.6.6/Trinity line 1616.

# No butterfly assemblies to report.

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

Left read files: $VAR1 = [
          '/scratch/lym_myl_rsch/mma/bracer_test/results/cell1/aligned_reads/cell1_BCR_K_1.fastq'
        ];
Right read files: $VAR1 = [
          '/scratch/lym_myl_rsch/mma/bracer_test/results/cell1/aligned_reads/cell1_BCR_K_2.fastq'
        ];
Trinity version: Trinity-v2.6.6
-ERROR: couldn't run the network check to confirm latest Trinity software version.

Tuesday, August 14, 2018: 11:20:03  CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /risapps/noarch/trinity/2.6.6/util/support_scripts/ExitTester.jar 0
Tuesday, August 14, 2018: 11:20:03  CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /risapps/noarch/trinity/2.6.6/util/support_scripts/ExitTester.jar 1
Tuesday, August 14, 2018: 11:20:04  CMD: mkdir -p /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K
Tuesday, August 14, 2018: 11:20:04  CMD: mkdir -p /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis

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

Converting input files. (in parallel)Tuesday, August 14, 2018: 11:20:04 CMD: cat /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/aligned_reads/cell1_BCR_K_1.fastq | seqtk-trinity seq -A - >> left.fa
Tuesday, August 14, 2018: 11:20:04  CMD: cat /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/aligned_reads/cell1_BCR_K_2.fastq | seqtk-trinity seq -A - >> right.fa
Tuesday, August 14, 2018: 11:20:04  CMD: touch left.fa.ok
Tuesday, August 14, 2018: 11:20:04  CMD: touch right.fa.ok
Tuesday, August 14, 2018: 11:20:04  CMD: touch left.fa.ok right.fa.ok
Tuesday, August 14, 2018: 11:20:04  CMD: cat left.fa right.fa > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/both.fa
Tuesday, August 14, 2018: 11:20:04  CMD: touch /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/both.fa.ok
-------------------------------------------
----------- Jellyfish  --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

* Running CMD: jellyfish count -t 4 -m 25 -s 100000000  --canonical  /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/both.fa
* Running CMD: jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa
* Running CMD: jellyfish histo -t 4 -o jellyfish.kmers.fa.histo mer_counts.jf
----------------------------------------------
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------

* Running CMD: /risapps/noarch/trinity/2.6.6/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1   --DS  --num_threads 4  --PARALLEL_IWORM  > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/inchworm.K25.L25.DS.fa.tmp
* Running CMD: mv /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/inchworm.K25.L25.DS.fa.tmp /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/inchworm.K25.L25.DS.fa
Tuesday, August 14, 2018: 11:20:05  CMD: touch /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/inchworm.K25.L25.DS.fa.finished
--------------------------------------------------------
-------------------- Chrysalis -------------------------
-- (Contig Clustering & de Bruijn Graph Construction) --
--------------------------------------------------------

inchworm_target: /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/both.fa
bowite_reads_fa: /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/both.fa
chrysalis_reads_fa: /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/both.fa
* Running CMD: /risapps/noarch/trinity/2.6.6/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/inchworm.K25.L25.DS.fa 100 10 > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/inchworm.K25.L25.DS.fa.min100
* Running CMD: /risapps/noarch/bowtie2/2.3.4.2/bowtie2-build --threads 4 -o 3 /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/inchworm.K25.L25.DS.fa.min100 /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/inchworm.K25.L25.DS.fa.min100 1>/dev/null
* Running CMD: bash -c " set -o pipefail;/risapps/noarch/bowtie2/2.3.4.2/bowtie2 --local -k 2 --no-unal --threads 4 -f --score-min G,20,4 -x /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/inchworm.K25.L25.DS.fa.min100 /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/both.fa  | samtools view -@ 4 -F4 -Sb - | samtools sort -m 536870912 -@ 4 -no - - > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/iworm.bowtie.nameSorted.bam" 
* Running CMD: /risapps/noarch/trinity/2.6.6/util/support_scripts/scaffold_iworm_contigs.pl /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/iworm.bowtie.nameSorted.bam /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/inchworm.K25.L25.DS.fa > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/iworm_scaffolds.txt
* Running CMD: /risapps/noarch/trinity/2.6.6/Chrysalis/GraphFromFasta -i /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/inchworm.K25.L25.DS.fa -r /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 4 -k 24 -kk 48  > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/iworm_cluster_welds_graph.txt
* Running CMD: /risapps/noarch/trinity/2.6.6/Chrysalis/BubbleUpClustering -i /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/inchworm.K25.L25.DS.fa  -weld_graph /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/iworm_cluster_welds_graph.txt -min_contig_length 200  > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/GraphFromIwormFasta.out
* Running CMD: /risapps/noarch/trinity/2.6.6/Chrysalis/CreateIwormFastaBundle -i /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/GraphFromIwormFasta.out -o /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/bundled_iworm_contigs.fasta -min 200
* Running CMD: /risapps/noarch/trinity/2.6.6/Chrysalis/ReadsToTranscripts -i /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/both.fa -f /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/bundled_iworm_contigs.fasta -o /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/readsToComponents.out -t 4 -max_mem_reads 50000000 
* Running CMD: /bin/sort -T . -S 4G -k 1,1n /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/readsToComponents.out > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/chrysalis/readsToComponents.out.sort
Tuesday, August 14, 2018: 11:20:08  CMD: mkdir -p /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/read_partitions/Fb_0/CBin_0
Tuesday, August 14, 2018: 11:20:08  CMD: touch /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/partitioned_reads.files.list.ok
Tuesday, August 14, 2018: 11:20:08  CMD: /risapps/noarch/trinity/2.6.6/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --seqType fa --trinity_complete --full_cleanup  > recursive_trinity.cmds
Tuesday, August 14, 2018: 11:20:08  CMD: touch recursive_trinity.cmds.ok
Tuesday, August 14, 2018: 11:20:08  CMD: touch recursive_trinity.cmds.ok

--------------------------------------------------------------------------------
------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
--------------------------------------------------------------------------------

Tuesday, August 14, 2018: 11:20:08  CMD: /risapps/noarch/trinity/2.6.6/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 4 -v -shuffle 
Number of Commands: 1

succeeded(1)   100% completed.    

All commands completed successfully. :-)

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

Tuesday, August 14, 2018: 11:20:14  CMD: find /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/read_partitions/ -name '*inity.fasta'  | /risapps/noarch/trinity/2.6.6/util/support_scripts/partitioned_trinity_aggregator.pl TRINITY_DN > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/Trinity.fasta.tmp
Tuesday, August 14, 2018: 11:20:14  CMD: mv /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K/Trinity.fasta.tmp /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K.Trinity.fasta

###################################################################
Butterfly assemblies are written to /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K.Trinity.fasta
###################################################################

Tuesday, August 14, 2018: 11:20:14  CMD: /risapps/noarch/trinity/2.6.6/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K.Trinity.fasta > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_K.Trinity.fasta.gene_trans_map

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

Left read files: $VAR1 = [
          '/scratch/lym_myl_rsch/mma/bracer_test/results/cell1/aligned_reads/cell1_BCR_L_1.fastq'
        ];
Right read files: $VAR1 = [
          '/scratch/lym_myl_rsch/mma/bracer_test/results/cell1/aligned_reads/cell1_BCR_L_2.fastq'
        ];
Trinity version: Trinity-v2.6.6
-ERROR: couldn't run the network check to confirm latest Trinity software version.

Tuesday, August 14, 2018: 11:20:14  CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /risapps/noarch/trinity/2.6.6/util/support_scripts/ExitTester.jar 0
Tuesday, August 14, 2018: 11:20:15  CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /risapps/noarch/trinity/2.6.6/util/support_scripts/ExitTester.jar 1
Tuesday, August 14, 2018: 11:20:15  CMD: mkdir -p /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L
Tuesday, August 14, 2018: 11:20:15  CMD: mkdir -p /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis

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

Converting input files. (in parallel)Tuesday, August 14, 2018: 11:20:15 CMD: cat /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/aligned_reads/cell1_BCR_L_1.fastq | seqtk-trinity seq -A - >> left.fa
Tuesday, August 14, 2018: 11:20:15  CMD: cat /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/aligned_reads/cell1_BCR_L_2.fastq | seqtk-trinity seq -A - >> right.fa
Tuesday, August 14, 2018: 11:20:15  CMD: touch right.fa.ok
Tuesday, August 14, 2018: 11:20:15  CMD: touch left.fa.ok
Tuesday, August 14, 2018: 11:20:15  CMD: touch left.fa.ok right.fa.ok
Tuesday, August 14, 2018: 11:20:15  CMD: cat left.fa right.fa > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/both.fa
Tuesday, August 14, 2018: 11:20:15  CMD: touch /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/both.fa.ok
-------------------------------------------
----------- Jellyfish  --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

* Running CMD: jellyfish count -t 4 -m 25 -s 100000000  --canonical  /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/both.fa
* Running CMD: jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa
* Running CMD: jellyfish histo -t 4 -o jellyfish.kmers.fa.histo mer_counts.jf
----------------------------------------------
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------

* Running CMD: /risapps/noarch/trinity/2.6.6/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1   --DS  --num_threads 4  --PARALLEL_IWORM  > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/inchworm.K25.L25.DS.fa.tmp
* Running CMD: mv /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/inchworm.K25.L25.DS.fa.tmp /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/inchworm.K25.L25.DS.fa
Tuesday, August 14, 2018: 11:20:16  CMD: touch /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/inchworm.K25.L25.DS.fa.finished
--------------------------------------------------------
-------------------- Chrysalis -------------------------
-- (Contig Clustering & de Bruijn Graph Construction) --
--------------------------------------------------------

inchworm_target: /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/both.fa
bowite_reads_fa: /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/both.fa
chrysalis_reads_fa: /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/both.fa
* Running CMD: /risapps/noarch/trinity/2.6.6/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/inchworm.K25.L25.DS.fa 100 10 > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/inchworm.K25.L25.DS.fa.min100
* Running CMD: /risapps/noarch/bowtie2/2.3.4.2/bowtie2-build --threads 4 -o 3 /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/inchworm.K25.L25.DS.fa.min100 /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/inchworm.K25.L25.DS.fa.min100 1>/dev/null
* Running CMD: bash -c " set -o pipefail;/risapps/noarch/bowtie2/2.3.4.2/bowtie2 --local -k 2 --no-unal --threads 4 -f --score-min G,20,4 -x /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/inchworm.K25.L25.DS.fa.min100 /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/both.fa  | samtools view -@ 4 -F4 -Sb - | samtools sort -m 536870912 -@ 4 -no - - > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/iworm.bowtie.nameSorted.bam" 
* Running CMD: /risapps/noarch/trinity/2.6.6/util/support_scripts/scaffold_iworm_contigs.pl /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/iworm.bowtie.nameSorted.bam /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/inchworm.K25.L25.DS.fa > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/iworm_scaffolds.txt
* Running CMD: /risapps/noarch/trinity/2.6.6/Chrysalis/GraphFromFasta -i /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/inchworm.K25.L25.DS.fa -r /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 4 -k 24 -kk 48  > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/iworm_cluster_welds_graph.txt
* Running CMD: /risapps/noarch/trinity/2.6.6/Chrysalis/BubbleUpClustering -i /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/inchworm.K25.L25.DS.fa  -weld_graph /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/iworm_cluster_welds_graph.txt -min_contig_length 200  > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/GraphFromIwormFasta.out
* Running CMD: /risapps/noarch/trinity/2.6.6/Chrysalis/CreateIwormFastaBundle -i /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/GraphFromIwormFasta.out -o /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/bundled_iworm_contigs.fasta -min 200
* Running CMD: /risapps/noarch/trinity/2.6.6/Chrysalis/ReadsToTranscripts -i /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/both.fa -f /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/bundled_iworm_contigs.fasta -o /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/readsToComponents.out -t 4 -max_mem_reads 50000000 
* Running CMD: /bin/sort -T . -S 4G -k 1,1n /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/readsToComponents.out > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/chrysalis/readsToComponents.out.sort
Tuesday, August 14, 2018: 11:20:20  CMD: mkdir -p /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/read_partitions/Fb_0/CBin_0
Tuesday, August 14, 2018: 11:20:20  CMD: touch /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/partitioned_reads.files.list.ok
Tuesday, August 14, 2018: 11:20:20  CMD: /risapps/noarch/trinity/2.6.6/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --seqType fa --trinity_complete --full_cleanup  > recursive_trinity.cmds
Tuesday, August 14, 2018: 11:20:20  CMD: touch recursive_trinity.cmds.ok
Tuesday, August 14, 2018: 11:20:20  CMD: touch recursive_trinity.cmds.ok

--------------------------------------------------------------------------------
------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
--------------------------------------------------------------------------------

Tuesday, August 14, 2018: 11:20:20  CMD: /risapps/noarch/trinity/2.6.6/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 4 -v -shuffle 
Number of Commands: 1

succeeded(1)   100% completed.    

All commands completed successfully. :-)

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

Tuesday, August 14, 2018: 11:20:33  CMD: find /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/read_partitions/ -name '*inity.fasta'  | /risapps/noarch/trinity/2.6.6/util/support_scripts/partitioned_trinity_aggregator.pl TRINITY_DN > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/Trinity.fasta.tmp
Tuesday, August 14, 2018: 11:20:33  CMD: mv /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L/Trinity.fasta.tmp /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L.Trinity.fasta

###################################################################
Butterfly assemblies are written to /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L.Trinity.fasta
###################################################################

Tuesday, August 14, 2018: 11:20:33  CMD: /risapps/noarch/trinity/2.6.6/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L.Trinity.fasta > /scratch/lym_myl_rsch/mma/bracer_test/results/cell1/Trinity_output/Trinity_cell1_BCR_L.Trinity.fasta.gene_trans_map
       START> MakeDB
     ALIGNER> IgBLAST
ALIGNER_FILE> cell1_BCR_H.fmt7
    SEQ_FILE> cell1_BCR_H.Trinity.fasta
     PARTIAL> False
      SCORES> True
     REGIONS> True
     ASIS_ID> False
  ASIS_CALLS> False

PROGRESS> 11:20:45 |Loading files       | 0.0 min
PROGRESS> 11:20:45 |Done                | 0.0 min

PROGRESS> 11:20:45 |                    |   0% (0) 0.0 min
PROGRESS> 11:20:45 |##########          |  50% (1) 0.0 min
PROGRESS> 11:20:45 |####################| 100% (2) 0.0 min

OUTPUT> cell1_BCR_H_db-pass.tab
  PASS> 1
  FAIL> 1
   END> MakeDb

       START> MakeDB
     ALIGNER> IgBLAST
ALIGNER_FILE> cell1_BCR_K.fmt7
    SEQ_FILE> cell1_BCR_K.Trinity.fasta
     PARTIAL> False
      SCORES> True
     REGIONS> True
     ASIS_ID> False
  ASIS_CALLS> False

PROGRESS> 11:20:45 |Loading files       | 0.0 min
PROGRESS> 11:20:45 |Done                | 0.0 min

PROGRESS> 11:20:45 |                    |   0% (0) 0.0 min
PROGRESS> 11:20:45 |####################| 100% (1) 0.0 min

OUTPUT> cell1_BCR_K_db-pass.tab
  PASS> 1
  FAIL> 0
   END> MakeDb

       START> MakeDB
     ALIGNER> IgBLAST
ALIGNER_FILE> cell1_BCR_L.fmt7
    SEQ_FILE> cell1_BCR_L.Trinity.fasta
     PARTIAL> False
      SCORES> True
     REGIONS> True
     ASIS_ID> False
  ASIS_CALLS> False

PROGRESS> 11:20:46 |Loading files       | 0.0 min
PROGRESS> 11:20:46 |Done                | 0.0 min

PROGRESS> 11:20:46 |                    |   0% (0) 0.0 min
PROGRESS> 11:20:46 |####################| 100% (1) 0.0 min

OUTPUT> cell1_BCR_L_db-pass.tab
  PASS> 1
  FAIL> 0
   END> MakeDb

##Finding recombinant-derived reads##
Attempting new assembly for ['BCR_H', 'BCR_K', 'BCR_L']

Detected average R1 read length: 
50.0
Short read length detected. BraCeR will run two rounds of alignment for heavy chain

##BCR_H##
##BCR_K##
##BCR_L##

##Assembling Trinity Contigs##
##BCR_H##
Trinity failed for locus
##BCR_K##
##BCR_L##

##Running BLAST##
Performing Blast on ['BCR_H', 'BCR_K', 'BCR_L']
##BCR_H##
##BCR_K##
##BCR_L##

##Running IgBLAST##
Ig_seqtype: Ig
Performing IgBlast on ['BCR_H', 'BCR_K', 'BCR_L']
##BCR_H##
##BCR_K##
##BCR_L##

Traceback (most recent call last):
  File "/scratch/lym_myl_rsch/mma/.local/lib/python3.6/site-packages/Bio/Data/CodonTable.py", line 399, in __getitem__
    self.ambiguous_nucleotide)
  File "/scratch/lym_myl_rsch/mma/.local/lib/python3.6/site-packages/Bio/Data/CodonTable.py", line 214, in list_possible_proteins
    x1 = ambiguous_nucleotide_values[c1]
KeyError: '0'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/scratch/lym_myl_rsch/mma/.local/lib/python3.6/site-packages/Bio/Seq.py", line 2588, in _translate_str
    amino_acids.append(forward_table[codon])
  File "/scratch/lym_myl_rsch/mma/.local/lib/python3.6/site-packages/Bio/Data/CodonTable.py", line 402, in __getitem__
    raise KeyError(codon)  # stop codon
KeyError: '0.9'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/risapps/rhel6/python/3.6/bin/bracer", line 11, in <module>
    load_entry_point('bracer==0.1', 'console_scripts', 'bracer')()
  File "/risapps/rhel6/python/3.6/lib/python3.6/site-packages/bracer-0.1-py3.6.egg/bracerlib/launcher.py", line 43, in launch
    Task().run()
  File "/risapps/rhel6/python/3.6/lib/python3.6/site-packages/bracer-0.1-py3.6.egg/bracerlib/tasks.py", line 1945, in run
    trimmed_fastq2=self.trimmed_fastq2).run()
  File "/risapps/rhel6/python/3.6/lib/python3.6/site-packages/bracer-0.1-py3.6.egg/bracerlib/tasks.py", line 366, in run
    cell = self.ig_blast()
  File "/risapps/rhel6/python/3.6/lib/python3.6/site-packages/bracer-0.1-py3.6.egg/bracerlib/tasks.py", line 539, in ig_blast
    self.max_junc_len)
  File "/risapps/rhel6/python/3.6/lib/python3.6/site-packages/bracer-0.1-py3.6.egg/bracerlib/io.py", line 129, in parse_IgBLAST
    loci, max_junc_len, assembled_file)
  File "/risapps/rhel6/python/3.6/lib/python3.6/site-packages/bracer-0.1-py3.6.egg/bracerlib/bracer_func.py", line 348, in find_possible_alignments
    cdr3 = Seq(str(cdr3_seq), generic_dna).translate()
  File "/scratch/lym_myl_rsch/mma/.local/lib/python3.6/site-packages/Bio/Seq.py", line 1163, in translate
    cds, gap=gap)
  File "/scratch/lym_myl_rsch/mma/.local/lib/python3.6/site-packages/Bio/Seq.py", line 2605, in _translate_str
    "Codon '{0}' is invalid".format(codon))
Bio.Data.CodonTable.TranslationError: Codon '0.9' is invalid

The error seems to be from Biopython. Can you confirm 1.7.0 is the one to use?

JohnMCMa commented 6 years ago

Seems to be a side effect of not cleaning up the result directory properly... Closing.