[Errno 2] No such file or directory

[danielyao12]

Hi,

I tried to assemble the orthologs by using the aTRAM, which the orhologs were identified by orthofinder2 and included 3380 orthologs (in amino acid) as a multifasta file. The aTRAM command I used was:
/data/software/aTRAM/atram.py --cpus 10 -p \\ --temp-dir=/data/backbone_tree/dqgg_analysis/atram_analysis/dqgg0001_temp --keep-temp-dir \\ --path=~/anaconda3/envs/atram-env/bin \\ --blast-db=dqgg0001_output/DQGG0001 \\ -Q=3380ogs_polyneura_header.fa \\ --assembler=abyss \\ --output-prefix=dqgg0001_output/DQGG0001_atram

The temp folder "dqgg0001_temp" has been created before I ran the aTRAM command. I also looked at #308, #298, and #311 , but I still got the error message. Could you please have a look at my problem? How should I do to fix it?

Thank you for your!

Here are the error message I got:

( 49990) 2022-07-02 22:53:49.584221 INFO : ################################################################################
( 49990) 2022-07-02 22:53:49.584363 INFO : aTRAM version: v2.4.4
( 49990) 2022-07-02 22:53:49.584421 INFO : Python version: 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:18) [GCC 10.3.0]
( 49990) 2022-07-02 22:53:49.584467 INFO : /data/software/aTRAM/atram.py --cpus 10 -p --temp-dir=/data/backbone_tree/dqgg_analysis/atram_analysis/dqgg0001_temp --keep-temp-dir --path=/anaconda3/envs/atram-env/bin --blast-db=dqgg0001_output/DQGG0001 -Q=3380ogs_polyneura_header.fa --assembler=abyss --output-prefix=dqgg0001_output/DQGG0001_atram
( 49990) 2022-07-02 22:53:49.584559 INFO : aTRAM blast DB = "dqgg0001_output/DQGG0001", query = "3380ogs_polyneura_header_ILEX1_1.fasta", iteration 1
( 49990) 2022-07-02 22:53:49.584908 INFO : Blasting query against shards: iteration 1
( 49990) 2022-07-02 22:54:15.723124 INFO : All 59 blast results completed
( 49990) 2022-07-02 22:54:15.723949 INFO : 119 blast hits in iteration 1
( 49990) 2022-07-02 22:54:15.724050 INFO : Writing assembler input files: iteration 1
( 49990) 2022-07-02 22:54:15.743702 INFO : Assembling shards with abyss: iteration 1
( 49990) 2022-07-02 22:54:15.813399 ERROR: Exception: [Errno 2] No such file or directory: '/data/backbone_tree/dqgg_analysis/atram_analysis/dqgg0001_temp/atram_ngyw_1fc/DQGG0001_3380ogs_polyneura_header_ILEX1_1.fasta_01_n4y6bs_u/output.fasta-unitigs.fa'
( 49990) 2022-07-02 22:54:15.813962 INFO : Writing 0 filtered contigs after iteration 1
( 49990) 2022-07-02 22:54:15.814117 INFO : 0 total contigs after iteration 1
( 49990) 2022-07-02 22:54:15.824695 INFO : ################################################################################
( 49990) 2022-07-02 22:54:15.824825 INFO : aTRAM version: v2.4.4
( 49990) 2022-07-02 22:54:15.824904 INFO : Python version: 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:18) [GCC 10.3.0]
( 49990) 2022-07-02 22:54:15.824973 INFO : /data/software/aTRAM/atram.py --cpus 10 -p --temp-dir=/data/backbone_tree/dqgg_analysis/atram_analysis/dqgg0001_temp --keep-temp-dir --path=/anaconda3/envs/atram-env/bin --blast-db=dqgg0001_output/DQGG0001 -Q=3380ogs_polyneura_header.fa --assembler=abyss --output-prefix=dqgg0001_output/DQGG0001_atram
( 49990) 2022-07-02 22:54:15.825113 INFO : aTRAM blast DB = "dqgg0001_output/DQGG0001", query = "3380ogs_polyneura_header_ILEX2_2.fasta", iteration 1
( 49990) 2022-07-02 22:54:15.825621 INFO : Blasting query against shards: iteration 1
( 49990) 2022-07-02 22:54:40.473828 INFO : All 59 blast results completed
( 49990) 2022-07-02 22:54:40.474402 INFO : 54 blast hits in iteration 1
( 49990) 2022-07-02 22:54:40.474457 INFO : Writing assembler input files: iteration 1
( 49990) 2022-07-02 22:54:40.481769 INFO : Assembling shards with abyss: iteration 1
( 49990) 2022-07-02 22:54:40.517111 ERROR: Exception: [Errno 2] No such file or directory: '/data/backbone_tree/dqgg_analysis/atram_analysis/dqgg0001_temp/atram_ngyw_1fc/DQGG0001_3380ogs_polyneura_header_ILEX2_2.fasta_01_w3hepd6w/output.fasta-unitigs.fa'
( 49990) 2022-07-02 22:54:40.517357 INFO : Writing 0 filtered contigs after iteration 1
( 49990) 2022-07-02 22:54:40.517428 INFO : 0 total contigs after iteration 1
( 49990) 2022-07-02 22:54:40.525627 INFO : ################################################################################
( 49990) 2022-07-02 22:54:40.525672 INFO : aTRAM version: v2.4.4
( 49990) 2022-07-02 22:54:40.525701 INFO : Python version: 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:18) [GCC 10.3.0]
( 49990) 2022-07-02 22:54:40.525727 INFO : /data/software/aTRAM/atram.py --cpus 10 -p --temp-dir=/data/backbone_tree/dqgg_analysis/atram_analysis/dqgg0001_temp --keep-temp-dir --path=/anaconda3/envs/atram-env/bin --blast-db=dqgg0001_output/DQGG0001 -Q=3380ogs_polyneura_header.fa --assembler=abyss --output-prefix=dqgg0001_output/DQGG0001_atram
( 49990) 2022-07-02 22:54:40.525818 INFO : aTRAM blast DB = "dqgg0001_output/DQGG0001", query = "3380ogs_polyneura_header_ILEX3_3.fasta", iteration 1
( 49990) 2022-07-02 22:54:40.526283 INFO : Blasting query against shards: iteration 1
( 49990) 2022-07-02 22:55:12.838989 INFO : All 59 blast results completed
( 49990) 2022-07-02 22:55:12.839882 INFO : 241 blast hits in iteration 1
( 49990) 2022-07-02 22:55:12.839980 INFO : Writing assembler input files: iteration 1
( 49990) 2022-07-02 22:55:12.874383 INFO : Assembling shards with abyss: iteration 1
( 49990) 2022-07-02 22:55:12.944674 ERROR: Exception: [Errno 2] No such file or directory: '/data/backbone_tree/dqgg_analysis/atram_analysis/dqgg0001_temp/atram_ngyw_1fc/DQGG0001_3380ogs_polyneura_header_ILEX3_3.fasta_01_m1ilhzli/output.fasta-unitigs.fa'
( 49990) 2022-07-02 22:55:12.945272 INFO : Writing 0 filtered contigs after iteration 1
( 49990) 2022-07-02 22:55:12.945436 INFO : 0 total contigs after iteration 1
( 49990) 2022-07-02 22:55:12.956321 INFO : ################################################################################
( 49990) 2022-07-02 22:55:12.956437 INFO : aTRAM version: v2.4.4
( 49990) 2022-07-02 22:55:12.956513 INFO : Python version: 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:18) [GCC 10.3.0]
( 49990) 2022-07-02 22:55:12.956610 INFO : /data/software/aTRAM/atram.py --cpus 10 -p --temp-dir=/data/backbone_tree/dqgg_analysis/atram_analysis/dqgg0001_temp --keep-temp-dir --path=/anaconda3/envs/atram-env/bin --blast-db=dqgg0001_output/DQGG0001 -Q=3380ogs_polyneura_header.fa --assembler=abyss --output-prefix=dqgg0001_output/DQGG0001_atram
( 49990) 2022-07-02 22:55:12.956751 INFO : aTRAM blast DB = "dqgg0001_output/DQGG0001", query = "3380ogs_polyneura_header_ILEX4_4.fasta", iteration 1
( 49990) 2022-07-02 22:55:12.957279 INFO : Blasting query against shards: iteration 1
( 49990) 2022-07-02 22:55:39.778365 INFO : All 59 blast results completed
( 49990) 2022-07-02 22:55:39.779066 INFO : 152 blast hits in iteration 1
( 49990) 2022-07-02 22:55:39.779141 INFO : Writing assembler input files: iteration 1
( 49990) 2022-07-02 22:55:39.793642 INFO : Assembling shards with abyss: iteration 1
( 49990) 2022-07-02 22:55:39.862850 ERROR: Exception: [Errno 2] No such file or directory: '/data/backbone_tree/dqgg_analysis/atram_analysis/dqgg0001_temp/atram_ngyw_1fc/DQGG0001_3380ogs_polyneura_header_ILEX4_4.fasta_01_1x4x82wv/output.fasta-unitigs.fa'
( 49990) 2022-07-02 22:55:39.863340 INFO : Writing 0 filtered contigs after iteration 1
( 49990) 2022-07-02 22:55:39.863475 INFO : 0 total contigs after iteration 1
( 49990) 2022-07-02 22:55:39.874442 INFO : ################################################################################

[laiqiang0728]

I had a similar ERROR once, and I used the Trinity as the assembly tools, so the ERROR noted that “Exception: [Errno 2] No such file or directory: /path..../***.trinity.fasta”. I eventually found the problem was that the Trinity had not been installed correctly. So may be your ERROR also caused by the assembly tools.

Hope it's helpful for you!

[Erythroxylum]

@danielyao12
Did you ever find a fix for this issue? Thanks.