cat: ./Homo_mitoscaf.fa.genewise/*/*.genewise: No such file or directory #231
Description
When I execute the software to make annotations:
python3 ../MitoZ/version_2.4-alpha/release_MitoZ_v2.4-alpha/MitoZ.py annotate --genetic_code 2 --clade Chordata --outprefix Homo --thread_number 12 --fastafile sequence.fasta
The following content is the output
2025-05-08 16:09:00
export WISECONFIGDIR=/test_ann_MitoZ/MitoZ/version_2.4-alpha/release_MitoZ_v2.4-alpha/bin/annotate/wifg
perl /test_ann_MitoZ/MitoZ/version_2.4-alpha/release_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_32/MT_annotation_BGI.pl -i Homo_mitoscaf.fa -d /test_ann_MitoZ/MitoZ/version_2.4-alpha/release_MitoZ_4-alpha/bin/profiles/MT_database/Chordata_CDS_protein.fa -o ./ -g 2 -cpu 12
makeblastdb -in Homo_mitoscaf.fa -dbtype nucl
run the tblastn shell file
Run solar to conjoin HSPs and filter bad HSPs and redundance.
preparing genewise input directories and files
name gi_NC_KM273123_COX3_Drepane_punctata_261_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-alprelease_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 36059.
name gi_NC_KP164983_COX3_Drepane_longimana_261_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-al/release_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 40505.
name gi_NC_010292_CYTB_Heteronotia_binoei_379_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-alprelease_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 51239.
name gi_NC_019615_ND5_Hoplobatrachus_rugulosus_611_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.lpha/release_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 97575.
name gi_NC_027267_ND6_Phalacrocorax_carbo_173_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-alprelease_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 105007.
name gi_NC_018340_ND6_Champsocephalus_gunnari_174_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4pha/release_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 106795.
name gi_NC_025925_ND6_Ixobrychus_sinensis_173_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-alprelease_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 107345.
name gi_NC_025924_ND6_Ixobrychus_eurhythmus_173_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-aa/release_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 107349.
name gi_NC_025923_ND6_Botaurus_stellaris_173_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-alphelease_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 107353.
name gi_NC_025922_ND6_Butorides_striata_173_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-alphalease_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 107357.
name gi_NC_025921_ND6_Ardeola_bacchus_173_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-alpha/rase_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 107361.
name gi_NC_025920_ND6_Egretta_sacra_173_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-alpha/rele_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 107365.
name gi_NC_015087_ND6_Penelopides_panini_173_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-alphelease_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 107997.
name gi_NC_015085_ND6_Aceros_waldeni_173_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-alpha/rese_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 108001.
name gi_NC_029147_ND6_Turdus_philomelos_171_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-alphalease_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 109401.
name gi_NC_029140_ND6_Notiomystis_cincta_172_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-alphelease_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 109415.
name gi_NC_026190_ND6_Phoebastria_albatrus_175_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-al/release_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 109921.
name gi_NC_026189_ND6_Phoebastria_immutabilis_175_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4pha/release_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 109925.
name gi_NC_026188_ND6_Phoebastria_nigripes_175_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-al/release_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 109929.
name gi_NC_010292_ND6_Heteronotia_binoei_173_aa is not uniq at /test_ann_MitoZ/MitoZ/version_2.4-alphelease_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 111929.
name gi_NC_007172.2_ND6_Thalassarche_melanophrys_175_aa is not uniq at /test_ann_MitoZ/MitoZ/version_-alpha/release_MitoZ_v2.4-alpha/bin/annotate/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl line 240, line 112085.
run the genewise shell file
running genewise
convert result to gff3 format
cat: ./Homo_mitoscaf.fa.genewise//.genewise: No such file or directory
Sorry, the annotation finished with no result!
2025-05-09 14:45:08
rm -rf *.nhr *.nin *.nsq formatdb.log *.tblastn.shell *.length *.blast *.blast.filter *.shell *.blast.solar *.blast.solar.filter *.blasolar.filter.table *.blast.solar.filter.table.nonredundance *.blast.solar.filter.nr *.genewise *.solar.genewise.gff *.solar.genewise.gffs
2025-05-09 14:45:08
/opt/hschedd/bin/docker_jobsub/python3/bin/python3 /test_ann_MitoZ/MitoZ/version_2.4-alpha/release_Mi_v2.4-alpha/bin/annotate/prepare_CDSposition.py Homo_mitoscaf.fa.solar.genewise.gff.cds.position.cds Homo.cds.position
Traceback (most recent call last):
File "/test_ann_MitoZ/MitoZ/version_2.4-alpha/release_MitoZ_v2.4-alpha/bin/annotate/prepare_CDSposin.py", line 47, in
fh_in = open(in_f, 'r')
FileNotFoundError: [Errno 2] No such file or directory: 'Homo_mitoscaf.fa.solar.genewise.gff.cds.position.cds'
Error occured when running command:
/opt/hschedd/bin/docker_jobsub/python3/bin/python3 /test_ann_MitoZ/MitoZ/version_2.4-alpha/release_Mi_v2.4-alpha/bin/annotate/prepare_CDSposition.py Homo_mitoscaf.fa.solar.genewise.gff.cds.position.cds Homo.cds.position
I don't know why I got it,
cat: ./Homo_mitoscaf.fa.genewise//.genewise: No such file or directory
The input file I used is the human mitochondrial genome.
Thank you for your positive feedback. It's very important to me.