mstubb
commented
5 years ago Hi Stijn,
Are you using all built-in sequence references? It looks like the TRAV29_DV5*03 allele isn’t in https://github.com/Teichlab/tracer/blob/master/resources/Hsap/raw_seqs/TCR_A_V.fa https://github.com/Teichlab/tracer/blob/master/resources/Hsap/raw_seqs/TCR_A_V.fa so Tracer can’t extract the sequence to make a full-length version based on the reference. However, if it’s not in the reference, I’m a bit confused about why it’s being provided as an annotation by IgBLAST. I'd have to dive in and remember exactly how the references were set up.
In the meantime, can you run that cell with the -m assembly flag (detailed here https://github.com/Teichlab/tracer#options https://github.com/Teichlab/tracer#options) which I think will stop it trying to find the sequence in the references.
Let me know if any of that works. I’ll try to find time to dig in more but might not be for a little while, sorry.
Cheers,
Mike
On 13 May 2019, at 18:32, micans notifications@github.com wrote:
Hi, below is the KeyError error that I get with tracer assemble. It is only one out of 1536 samples, so otherwise the software is running very nicely. Below the error I have copied a listing of the output files that were generated; in particular the fastq files are non-empty (they are uncompressed into the files f1 and f2). I notice that the 'overall alignment rate' looks low (0.12%), but it's similar in other samples. Is this something I need to worry about? Let me know if there is a way to dig further into this, Thanks, Stijn
Error
924078 reads; of these: 924078 (100.00%) were paired; of these: 923196 (99.90%) aligned concordantly 0 times 882 (0.10%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times
923196 pairs aligned concordantly 0 times; of these: 22 (0.00%) aligned discordantly 1 time ---- 923174 pairs aligned 0 times concordantly or discordantly; of these: 1846348 mates make up the pairs; of these: 1845935 (99.98%) aligned 0 times 321 (0.02%) aligned exactly 1 time 92 (0.00%) aligned >1 times0.12% overall alignment rate 924078 reads; of these: 924078 (100.00%) were paired; of these: 922260 (99.80%) aligned concordantly 0 times 1818 (0.20%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times
922260 pairs aligned concordantly 0 times; of these: 6 (0.00%) aligned discordantly 1 time ---- 922254 pairs aligned 0 times concordantly or discordantly; of these: 1844508 mates make up the pairs; of these: 1843450 (99.94%) aligned 0 times 863 (0.05%) aligned exactly 1 time 195 (0.01%) aligned >1 times0.25% overall alignment rate Traceback (most recent call last): File "/usr/local/bin/tracer", line 11, in
load_entry_point('tracer==0.5', 'console_scripts', 'tracer')() File "/usr/local/lib/python3.5/dist-packages/tracer-0.5-py3.5.egg/tracerlib/launcher.py", line 43, in launch Task().run() File "/usr/local/lib/python3.5/dist-packages/tracer-0.5-py3.5.egg/tracerlib/tasks.py", line 372, in run cell = self.ig_blast() File "/usr/local/lib/python3.5/dist-packages/tracer-0.5-py3.5.egg/tracerlib/tasks.py", line 515, in ig_blast self.max_junc_len) File "/usr/local/lib/python3.5/dist-packages/tracer-0.5-py3.5.egg/tracerlib/io.py", line 113, in parse_IgBLAST loci, max_junc_len) File "/usr/local/lib/python3.5/dist-packages/tracer-0.5-py3.5.egg/tracerlib/tracer_func.py", line 213, in find_possible_alignments query_name, species, loci_for_segments) File "/usr/local/lib/python3.5/dist-packages/tracer-0.5-py3.5.egg/tracerlib/tracer_func.py", line 382, in get_fasta_line_for_contig_imgt best_V_seq = IMGT_seqs[V_locus_key][segment] KeyError: 'TRAV29_DV5*03' Directory structure: root@robin:/workspace/svd/work2/7d/140d7c90d67b9c1900e3ee491987da# find -maxdepth 3 -exec ls -l {} \; total 336591 lrwxrwxrwx 1 root root 55 May 13 12:50 Human_colon_16S7722453_1.fastq.gz -> /workspace/svd/fastqs/Human_colon_16S7722453_1.fastq.gz lrwxrwxrwx 1 root root 55 May 13 12:50 Human_colon_16S7722453_2.fastq.gz -> /workspace/svd/fastqs/Human_colon_16S7722453_2.fastq.gz -rw-r--r-- 1 root root 172334567 May 13 12:50 f1 -rw-r--r-- 1 root root 172334567 May 13 12:50 f2 drwxr-xr-x 3 root root 48 May 13 12:50 out_asm -rw-r--r-- 1 root root 235 May 13 12:50 ./.command.sh -rw-r--r-- 1 root root 3484 May 13 12:50 ./.command.stub -rw-r--r-- 1 root root 2274 May 13 12:50 ./.command.run -rw-r--r-- 1 root root 717 May 13 12:50 ./.command.yaml -rw-r--r-- 1 root root 0 May 13 12:50 ./.command.begin lrwxrwxrwx 1 root root 55 May 13 12:50 ./Human_colon_16S7722453_1.fastq.gz -> /workspace/svd/fastqs/Human_colon_16S7722453_1.fastq.gz lrwxrwxrwx 1 root root 55 May 13 12:50 ./Human_colon_16S7722453_2.fastq.gz -> /workspace/svd/fastqs/Human_colon_16S7722453_2.fastq.gz -rw-r--r-- 1 root root 24373 May 13 12:50 ./.command.out -rw-r--r-- 1 root root 2283 May 13 12:50 ./.command.err -rw-r--r-- 1 root root 194 May 13 12:51 ./.command.trace -rw-r--r-- 1 root root 172334567 May 13 12:50 ./f1 -rw-r--r-- 1 root root 172334567 May 13 12:50 ./f2 total 0 drwxr-xr-x 8 root root 184 May 13 12:50 out-Human_colon_16S7722453 total 4 drwxr-xr-x 2 root root 240 May 13 14:44 IgBLAST_output drwxr-xr-x 2 root root 218 May 13 12:50 Trinity_output drwxr-xr-x 2 root root 4096 May 13 12:50 aligned_reads drwxr-xr-x 2 root root 10 May 13 12:50 expression_quantification drwxr-xr-x 2 root root 10 May 13 12:50 filtered_TCR_seqs drwxr-xr-x 2 root root 10 May 13 12:50 unfiltered_TCR_seqs total 3499 -rw-r--r-- 1 root root 951335 May 13 12:50 out-Human_colon_16S7722453_TCR_A.sam -rw-r--r-- 1 root root 177160 May 13 12:50 out-Human_colon_16S7722453_TCR_A_1.fastq -rw-r--r-- 1 root root 177160 May 13 12:50 out-Human_colon_16S7722453_TCR_A_2.fastq -rw-r--r-- 1 root root 1558060 May 13 12:50 out-Human_colon_16S7722453_TCR_B.sam -rw-r--r-- 1 root root 358400 May 13 12:50 out-Human_colon_16S7722453_TCR_B_1.fastq -rw-r--r-- 1 root root 358400 May 13 12:50 out-Human_colon_16S7722453_TCR_B_2.fastq total 10 -rw-r--r-- 1 root root 5268 May 13 12:50 out-Human_colon_16S7722453_TCR_A.Trinity.fasta -rw-r--r-- 1 root root 3261 May 13 12:50 out-Human_colon_16S7722453_TCR_B.Trinity.fasta -rw-r--r-- 1 root root 51 May 13 12:50 successful_trinity_assemblies.txt -rw-r--r-- 1 root root 0 May 13 12:50 unsuccessful_trinity_assemblies.txt total 90 -rw-r--r-- 1 root root 15495 May 13 12:50 out-Human_colon_16S7722453_TCR_A.IgBLASTOut -rw-r--r-- 1 root root 41591 May 13 12:50 out-Human_colon_16S7722453_TCR_A_fmt3.IgBLASTOut -rw-r--r-- 1 root root 9746 May 13 12:50 out-Human_colon_16S7722453_TCR_B.IgBLASTOut -rw-r--r-- 1 root root 23827 May 13 12:50 out-Human_colon_16S7722453_TCR_B_fmt3.IgBLASTOut — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Teichlab/tracer/issues/90?email_source=notifications&email_token=AAIXBBTCX24B7W7ZBFSQKA3PVGJYNA5CNFSM4HMRP7S2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GTPFUXA, or mute the thread https://github.com/notifications/unsubscribe-auth/AAIXBBQADI64CPLJDBGOV63PVGJYNANCNFSM4HMRP7SQ.
micans
arielmadr
jfass
Hi, below is the KeyError error that I get with tracer assemble. It is only one out of 1536 samples, so otherwise the software is running very nicely. Below the error I have copied a listing of the output files that were generated; in particular the fastq files are non-empty (they are uncompressed into the files f1 and f2). I notice that the 'overall alignment rate' looks low (0.12%), but it's similar in other samples. Is this something I need to worry about? Let me know if there is a way to dig further into this, Thanks, Stijn
Error
Directory structure: