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timeout error in atram.py #304

Open senramvx opened 3 years ago

senramvx commented 3 years ago

Hi, I'm trying to use aTRAM to select orthologs from reads of some WGS projects, but I'm having an time out error while running atram.py. Any idea what may be causing this?

Thanks in advance for your attention.

(venv) marcus-senra@ubuntu:/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/Analyses$ python ../aTRAM/atram.py -b SRR8698590 -q '/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' -p -o SRR8698590 -a spades --cpus 8 -t temp --spades-threads 8 ( 18384) 2021-07-03 11:45:45.929699 INFO : ################################################################################ ( 18384) 2021-07-03 11:45:45.929880 INFO : aTRAM version: v2.4.3 ( 18384) 2021-07-03 11:45:45.929931 INFO : Python version: 3.8.10 (default, Jun 2 2021, 10:49:15) [GCC 9.4.0] ( 18384) 2021-07-03 11:45:45.929969 INFO : ../aTRAM/atram.py -b SRR8698590 -q /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta -p -o SRR8698590 -a spades --cpus 8 -t temp --spades-threads 8 ( 18384) 2021-07-03 11:45:45.930075 INFO : aTRAM blast DB = "SRR8698590", query = "OrthoDB_CIL8080_Clusterd95.fasta", iteration 1 ( 18384) 2021-07-03 11:45:45.930551 INFO : Blasting query against shards: iteration 1 ( 18388) 2021-07-03 11:55:45.953842 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.004.blast.results.json -db SRR8698590.004.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999005210011 seconds ( 18386) 2021-07-03 11:55:45.953869 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.002.blast.results.json -db SRR8698590.002.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999076519998 seconds ( 18389) 2021-07-03 11:55:45.953872 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.005.blast.results.json -db SRR8698590.005.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999099249999 seconds ( 18385) 2021-07-03 11:55:45.954274 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.001.blast.results.json -db SRR8698590.001.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999162629992 seconds ( 18391) 2021-07-03 11:55:45.954773 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.007.blast.results.json -db SRR8698590.007.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999300179988 seconds ( 18387) 2021-07-03 11:55:45.955537 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.003.blast.results.json -db SRR8698590.003.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999139369993 seconds ( 18390) 2021-07-03 11:55:45.958261 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.006.blast.results.json -db SRR8698590.006.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999167850001 seconds ( 18392) 2021-07-03 11:55:45.963240 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.008.blast.results.json -db SRR8698590.008.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999283789984 seconds ( 18390) 2021-07-03 11:55:45.978685 ERROR: Killed 2 processes with SIGTERM. ( 18392) 2021-07-03 11:55:45.979367 ERROR: Killed 2 processes with SIGTERM. ( 18391) 2021-07-03 11:55:45.979891 ERROR: Killed 2 processes with SIGTERM. ( 18386) 2021-07-03 11:55:45.980978 ERROR: Killed 2 processes with SIGTERM. ( 18389) 2021-07-03 11:55:45.984268 ERROR: Killed 2 processes with SIGTERM. ( 18385) 2021-07-03 11:55:45.985064 ERROR: Killed 2 processes with SIGTERM. ( 18387) 2021-07-03 11:55:45.985297 ERROR: Killed 2 processes with SIGTERM. ( 18388) 2021-07-03 11:55:45.985993 ERROR: Killed 2 processes with SIGTERM. ( 18384) 2021-07-03 11:55:46.011412 INFO : Writing 0 filtered contigs after iteration 1 ( 18384) 2021-07-03 11:55:46.013895 INFO : 0 total contigs after iteration 1

juliema commented 3 years ago

Hi. If you have multiple loci in the file 'OrthoDB_CIL8080_Clusterd95.fasta' then you want to use the -Q option rather than the -q option. it is likely aTRAM is blasting all of the sequences in that file to your library.

here is the code to try:

python ../aTRAM/atram.py -b SRR8698590 -Q '/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' -p -o SRR8698590 -a spades --cpus 8 -t temp --spades-threads 8

thanks

On Sat, Jul 3, 2021 at 11:07 AM senramvx @.***> wrote:

Hi, I'm trying to use aTRAM to select orthologs from reads of some WGS projects, but I'm having an time out error while running atram.py. Any idea what may be causing this?

Thanks in advance for your attention.

(venv) @.***:/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/Analyses$ python ../aTRAM/atram.py -b SRR8698590 -q '/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' -p -o SRR8698590 -a spades --cpus 8 -t temp --spades-threads 8 ( 18384) 2021-07-03 11:45:45.929699 INFO : ################################################################################ ( 18384) 2021-07-03 11:45:45.929880 INFO : aTRAM version: v2.4.3 ( 18384) 2021-07-03 11:45:45.929931 INFO : Python version: 3.8.10 (default, Jun 2 2021, 10:49:15) [GCC 9.4.0] ( 18384) 2021-07-03 11:45:45.929969 INFO : ../aTRAM/atram.py -b SRR8698590 -q /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta -p -o SRR8698590 -a spades --cpus 8 -t temp --spades-threads 8 ( 18384) 2021-07-03 11:45:45.930075 INFO : aTRAM blast DB = "SRR8698590", query = "OrthoDB_CIL8080_Clusterd95.fasta", iteration 1 ( 18384) 2021-07-03 11:45:45.930551 INFO : Blasting query against shards: iteration 1 ( 18388) 2021-07-03 11:55:45.953842 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.004.blast.results.json -db SRR8698590.004.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999005210011 seconds ( 18386) 2021-07-03 11:55:45.953869 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.002.blast.results.json -db SRR8698590.002.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999076519998 seconds ( 18389) 2021-07-03 11:55:45.953872 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.005.blast.results.json -db SRR8698590.005.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999099249999 seconds ( 18385) 2021-07-03 11:55:45.954274 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.001.blast.results.json -db SRR8698590.001.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999162629992 seconds ( 18391) 2021-07-03 11:55:45.954773 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.007.blast.results.json -db SRR8698590.007.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999300179988 seconds ( 18387) 2021-07-03 11:55:45.955537 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.003.blast.results.json -db SRR8698590.003.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999139369993 seconds ( 18390) 2021-07-03 11:55:45.958261 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.006.blast.results.json -db SRR8698590.006.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999167850001 seconds ( 18392) 2021-07-03 11:55:45.963240 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.008.blast.results.json -db SRR8698590.008.blast -query /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999283789984 seconds ( 18390) 2021-07-03 11:55:45.978685 ERROR: Killed 2 processes with SIGTERM. ( 18392) 2021-07-03 11:55:45.979367 ERROR: Killed 2 processes with SIGTERM. ( 18391) 2021-07-03 11:55:45.979891 ERROR: Killed 2 processes with SIGTERM. ( 18386) 2021-07-03 11:55:45.980978 ERROR: Killed 2 processes with SIGTERM. ( 18389) 2021-07-03 11:55:45.984268 ERROR: Killed 2 processes with SIGTERM. ( 18385) 2021-07-03 11:55:45.985064 ERROR: Killed 2 processes with SIGTERM. ( 18387) 2021-07-03 11:55:45.985297 ERROR: Killed 2 processes with SIGTERM. ( 18388) 2021-07-03 11:55:45.985993 ERROR: Killed 2 processes with SIGTERM. ( 18384) 2021-07-03 11:55:46.011412 INFO : Writing 0 filtered contigs after iteration 1 ( 18384) 2021-07-03 11:55:46.013895 INFO : 0 total contigs after iteration 1

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senramvx commented 3 years ago

Hi, Thanks for your reply. It solved the problem. However, there is another error message (Exception: [Errno 2] ) coming up. Besides that, contigs.fasta files are being written anyway (as shown below). Is this something I should be worried about?

Thanks again in advance.

Best regards,

Marcus

(venv) @.:/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/Analyses$ ../aTRAM/atram.py -b SRR8698590 -Q '/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/Cluster95.fa' --blast-db-gencode 6 -o SRR8698590 -a spades --cpus 8 -t temp/ --no-filter --blast-max-target-seqs 1 --spades-threads 8 --spades-memory 12 ( 103088) 2021-07-13 18:16:46.641090 INFO : ################################################################################ ( 103088) 2021-07-13 18:16:46.641270 INFO : aTRAM version: v2.4.3 ( 103088) 2021-07-13 18:16:46.641314 INFO : Python version: 3.8.10 (default, Jun 2 2021, 10:49:15) [GCC 9.4.0] ( 103088) 2021-07-13 18:16:46.641348 INFO : ../aTRAM/atram.py -b SRR8698590 -Q /media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/Cluster95.fa --blast-db-gencode 6 -o SRR8698590 -a spades --cpus 8 -t temp/ --no-filter --blast-max-target-seqs 1 --spades-threads 8 --spades-memory 12 ( 103088) 2021-07-13 18:16:46.641445 INFO : aTRAM blast DB = "SRR8698590", query = "Cluster95_5963_1_000129_1.fasta", iteration 1 ( 103088) 2021-07-13 18:16:46.641850 INFO : Blasting query against shards: iteration 1 ( 103088) 2021-07-13 18:17:09.050754 INFO : All 17 blast results completed ( 103088) 2021-07-13 18:17:09.051455 INFO : 17 blast hits in iteration 1 ( 103088) 2021-07-13 18:17:09.051530 INFO : Writing assembler input files: iteration 1 ( 103088) 2021-07-13 18:17:09.056079 INFO : Assembling shards with spades: iteration 1 ( 103088) 2021-07-13 18:17:10.524410 INFO : Saving assembled contigs: iteration 1 ( 103088) 2021-07-13 18:17:10.668631 INFO : Creating new query files: iteration 1 ( 103088) 2021-07-13 18:17:10.674083 INFO : aTRAM blast DB = "SRR8698590", query = "SRR8698590_Cluster95_5963_1_000129_1.fasta_01_long_reads.fasta", iteration 2 ( 103088) 2021-07-13 18:17:10.674528 INFO : Blasting query against shards: iteration 2 ( 103088) 2021-07-13 18:17:12.985633 INFO : All 17 blast results completed ( 103088) 2021-07-13 18:17:12.986392 INFO : 17 blast hits in iteration 2 ( 103088) 2021-07-13 18:17:12.986493 INFO : Writing assembler input files: iteration 2 ( 103088) 2021-07-13 18:17:12.991075 INFO : Assembling shards with spades: iteration 2 ( 103088) 2021-07-13 18:17:13.408016 ERROR: Exception: [Errno 2] No such file or directory: 'temp/atram_e1cvuk1g/SRR8698590_Cluster95_5963_1_000129_1.fasta_02_50a_u30q/spades/contigs.fasta' ( 103088) 2021-07-13 18:17:13.408227 INFO : 1 total contigs after iteration 2 ( 103088) 2021-07-13 18:17:13.991566 INFO : ################################################################################ @.:/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/Analyses$ ls SRR8698590.001.blast.nhr SRR8698590.005.blast.nin SRR8698590.009.blast.nsq SRR8698590.014.blast.nhr SRR8698590.sqlite.db-shm SRR8698590.001.blast.nin SRR8698590.005.blast.nsq SRR8698590.010.blast.nhr SRR8698590.014.blast.nin SRR8698590.sqlite.db-wal SRR8698590.001.blast.nsq SRR8698590.006.blast.nhr SRR8698590.010.blast.nin SRR8698590.014.blast.nsq SRR8698590.SRR8698590_Cluster95_227321_1_000d8b_9.all_contigs.fasta SRR8698590.002.blast.nhr SRR8698590.006.blast.nin SRR8698590.010.blast.nsq SRR8698590.015.blast.nhr SRR8698590.SRR8698590_Cluster95_4577_0_007a6b_10.all_contigs.fasta SRR8698590.002.blast.nin SRR8698590.006.blast.nsq SRR8698590.011.blast.nhr SRR8698590.015.blast.nin SRR8698590.SRR8698590_Cluster95_5963_1_000129_1.all_contigs.fasta SRR8698590.002.blast.nsq SRR8698590.007.blast.nhr SRR8698590.011.blast.nin SRR8698590.015.blast.nsq SRR8698590.SRR8698590_Cluster95_5963_1_001cd3_4.all_contigs.fasta SRR8698590.003.blast.nhr SRR8698590.007.blast.nin SRR8698590.011.blast.nsq SRR8698590.016.blast.nhr SRR8698590.SRR8698590_Cluster95_5963_1_002947_3.all_contigs.fasta SRR8698590.003.blast.nin SRR8698590.007.blast.nsq SRR8698590.012.blast.nhr SRR8698590.016.blast.nin SRR8698590.SRR8698590_Cluster95_5963_1_0034af_5.all_contigs.fasta SRR8698590.003.blast.nsq SRR8698590.008.blast.nhr SRR8698590.012.blast.nin SRR8698590.016.blast.nsq SRR8698590.SRR8698590_Cluster95_5963_1_00723a_2.all_contigs.fasta SRR8698590.004.blast.nhr SRR8698590.008.blast.nin SRR8698590.012.blast.nsq SRR8698590.017.blast.nhr SRR8698590.SRR8698590_Cluster95_7719_0_001308_7.all_contigs.fasta SRR8698590.004.blast.nin SRR8698590.008.blast.nsq SRR8698590.013.blast.nhr SRR8698590.017.blast.nin SRR8698590.SRR8698590_OrthoDB_CIL8080_Clusterd95_5963_1_000129_1.all_contigs.fasta SRR8698590.004.blast.nsq SRR8698590.009.blast.nhr SRR8698590.013.blast.nin SRR8698590.017.blast.nsq temp SRR8698590.005.blast.nhr SRR8698590.009.blast.nin SRR8698590.013.blast.nsq SRR8698590.sqlite.db

Em ter., 6 de jul. de 2021 às 10:31, juliema @.***> escreveu:

Hi. If you have multiple loci in the file 'OrthoDB_CIL8080_Clusterd95.fasta' then you want to use the -Q option rather than the -q option. it is likely aTRAM is blasting all of the sequences in that file to your library.

here is the code to try:

python ../aTRAM/atram.py -b SRR8698590 -Q

'/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' -p -o SRR8698590 -a spades --cpus 8 -t temp --spades-threads 8

thanks

On Sat, Jul 3, 2021 at 11:07 AM senramvx @.***> wrote:

Hi, I'm trying to use aTRAM to select orthologs from reads of some WGS projects, but I'm having an time out error while running atram.py. Any idea what may be causing this?

Thanks in advance for your attention.

(venv) @.***:/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/Analyses$ python ../aTRAM/atram.py -b SRR8698590 -q

'/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' -p -o SRR8698590 -a spades --cpus 8 -t temp --spades-threads 8 ( 18384) 2021-07-03 11:45:45.929699 INFO :

################################################################################ ( 18384) 2021-07-03 11:45:45.929880 INFO : aTRAM version: v2.4.3 ( 18384) 2021-07-03 11:45:45.929931 INFO : Python version: 3.8.10 (default, Jun 2 2021, 10:49:15) [GCC 9.4.0] ( 18384) 2021-07-03 11:45:45.929969 INFO : ../aTRAM/atram.py -b SRR8698590 -q

/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta -p -o SRR8698590 -a spades --cpus 8 -t temp --spades-threads 8 ( 18384) 2021-07-03 11:45:45.930075 INFO : aTRAM blast DB = "SRR8698590", query = "OrthoDB_CIL8080_Clusterd95.fasta", iteration 1 ( 18384) 2021-07-03 11:45:45.930551 INFO : Blasting query against shards: iteration 1 ( 18388) 2021-07-03 11:55:45.953842 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out

temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.004.blast.results.json -db SRR8698590.004.blast -query

/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999005210011 seconds ( 18386) 2021-07-03 11:55:45.953869 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out

temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.002.blast.results.json -db SRR8698590.002.blast -query

/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999076519998 seconds ( 18389) 2021-07-03 11:55:45.953872 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out

temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.005.blast.results.json -db SRR8698590.005.blast -query

/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999099249999 seconds ( 18385) 2021-07-03 11:55:45.954274 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out

temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.001.blast.results.json -db SRR8698590.001.blast -query

/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999162629992 seconds ( 18391) 2021-07-03 11:55:45.954773 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out

temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.007.blast.results.json -db SRR8698590.007.blast -query

/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999300179988 seconds ( 18387) 2021-07-03 11:55:45.955537 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out

temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.003.blast.results.json -db SRR8698590.003.blast -query

/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999139369993 seconds ( 18390) 2021-07-03 11:55:45.958261 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out

temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.006.blast.results.json -db SRR8698590.006.blast -query

/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999167850001 seconds ( 18392) 2021-07-03 11:55:45.963240 ERROR: Exception: Command 'tblastn -db_gencode 1 -evalue 1e-10 -outfmt 15 -max_target_seqs 100000000 -out

temp/atram_n46jtscf/SRR8698590_OrthoDB_CIL8080_Clusterd95.fasta_01_nf6dfrz9/SRR8698590.008.blast.results.json -db SRR8698590.008.blast -query

/media/marcus-senra/LabWork/Running_Projects/Orthologs_Ciliates/aTRAM/AA_DATASET/OrthoDB_CIL8080_Clusterd95.fasta' timed out after 599.9999283789984 seconds ( 18390) 2021-07-03 11:55:45.978685 ERROR: Killed 2 processes with SIGTERM. ( 18392) 2021-07-03 11:55:45.979367 ERROR: Killed 2 processes with SIGTERM. ( 18391) 2021-07-03 11:55:45.979891 ERROR: Killed 2 processes with SIGTERM. ( 18386) 2021-07-03 11:55:45.980978 ERROR: Killed 2 processes with SIGTERM. ( 18389) 2021-07-03 11:55:45.984268 ERROR: Killed 2 processes with SIGTERM. ( 18385) 2021-07-03 11:55:45.985064 ERROR: Killed 2 processes with SIGTERM. ( 18387) 2021-07-03 11:55:45.985297 ERROR: Killed 2 processes with SIGTERM. ( 18388) 2021-07-03 11:55:45.985993 ERROR: Killed 2 processes with SIGTERM. ( 18384) 2021-07-03 11:55:46.011412 INFO : Writing 0 filtered contigs after iteration 1 ( 18384) 2021-07-03 11:55:46.013895 INFO : 0 total contigs after iteration 1

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-- Marcus Senra, PhD

Post-Doctoral Fellowship on Molecular Genetics and Evolution of Microorganisms

UNIFEI - Brazil