[2024-01-24 13:37:24,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:24,959] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:24,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f1e762f-3d44-45a8-bdaf-6118f167e66e/dqc_reference
[2024-01-24 13:37:26,044] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:26,044] [INFO] Task started: Prodigal
[2024-01-24 13:37:26,045] [INFO] Running command: gunzip -c /var/lib/cwl/stg13d067d8-bba6-4594-8fc5-38e7afcd7755/GCF_000426465.1_ASM42646v1_genomic.fna.gz | prodigal -d GCF_000426465.1_ASM42646v1_genomic.fna/cds.fna -a GCF_000426465.1_ASM42646v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:40,462] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:40,463] [INFO] Task started: HMMsearch
[2024-01-24 13:37:40,463] [INFO] Running command: hmmsearch --tblout GCF_000426465.1_ASM42646v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f1e762f-3d44-45a8-bdaf-6118f167e66e/dqc_reference/reference_markers.hmm GCF_000426465.1_ASM42646v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:40,868] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:40,869] [INFO] Found 6/6 markers.
[2024-01-24 13:37:40,902] [INFO] Query marker FASTA was written to GCF_000426465.1_ASM42646v1_genomic.fna/markers.fasta
[2024-01-24 13:37:40,903] [INFO] Task started: Blastn
[2024-01-24 13:37:40,903] [INFO] Running command: blastn -query GCF_000426465.1_ASM42646v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f1e762f-3d44-45a8-bdaf-6118f167e66e/dqc_reference/reference_markers.fasta -out GCF_000426465.1_ASM42646v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:41,492] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:41,495] [INFO] Selected 13 target genomes.
[2024-01-24 13:37:41,495] [INFO] Target genome list was writen to GCF_000426465.1_ASM42646v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:41,499] [INFO] Task started: fastANI
[2024-01-24 13:37:41,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg13d067d8-bba6-4594-8fc5-38e7afcd7755/GCF_000426465.1_ASM42646v1_genomic.fna.gz --refList GCF_000426465.1_ASM42646v1_genomic.fna/target_genomes.txt --output GCF_000426465.1_ASM42646v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:51,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:51,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f1e762f-3d44-45a8-bdaf-6118f167e66e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:51,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f1e762f-3d44-45a8-bdaf-6118f167e66e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:51,145] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:51,145] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:51,145] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Epilithonimonas caeni	strain=DSM 17710	GCA_000426465.1	365343	365343	type	True	100.0	1363	1364	95	conclusive
Epilithonimonas hungarica	strain=DSM 19684	GCA_900102265.1	454006	454006	type	True	90.3525	1068	1364	95	below_threshold
Epilithonimonas hispanica	strain=KCTC 22104	GCA_003385395.1	358687	358687	type	True	84.1077	741	1364	95	below_threshold
Epilithonimonas zeae	strain=DSM 27623	GCA_900141765.1	1416779	1416779	type	True	83.918	871	1364	95	below_threshold
Epilithonimonas arachidiradicis	strain=DSM 27620	GCA_003610695.1	1617282	1617282	type	True	83.7362	828	1364	95	below_threshold
Epilithonimonas arachidiradicis	strain=CCM 8490	GCA_014635405.1	1617282	1617282	type	True	83.7058	822	1364	95	below_threshold
Epilithonimonas vandammei	strain=F5649	GCA_003860525.1	2487072	2487072	type	True	82.3775	628	1364	95	below_threshold
Epilithonimonas xixisoli	strain=CGMCC 1.12802	GCA_004365655.1	1476462	1476462	type	True	81.1909	681	1364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:51,146] [INFO] DFAST Taxonomy check result was written to GCF_000426465.1_ASM42646v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:51,147] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:51,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:51,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f1e762f-3d44-45a8-bdaf-6118f167e66e/dqc_reference/checkm_data
[2024-01-24 13:37:51,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:51,189] [INFO] Task started: CheckM
[2024-01-24 13:37:51,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000426465.1_ASM42646v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000426465.1_ASM42646v1_genomic.fna/checkm_input GCF_000426465.1_ASM42646v1_genomic.fna/checkm_result
[2024-01-24 13:38:34,713] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:34,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:34,728] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:34,729] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:34,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000426465.1_ASM42646v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:34,729] [INFO] Task started: Blastn
[2024-01-24 13:38:34,729] [INFO] Running command: blastn -query GCF_000426465.1_ASM42646v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f1e762f-3d44-45a8-bdaf-6118f167e66e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000426465.1_ASM42646v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:35,550] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:35,554] [INFO] Selected 10 target genomes.
[2024-01-24 13:38:35,554] [INFO] Target genome list was writen to GCF_000426465.1_ASM42646v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:35,573] [INFO] Task started: fastANI
[2024-01-24 13:38:35,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg13d067d8-bba6-4594-8fc5-38e7afcd7755/GCF_000426465.1_ASM42646v1_genomic.fna.gz --refList GCF_000426465.1_ASM42646v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000426465.1_ASM42646v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:44,360] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:44,367] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:44,367] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000426465.1	s__Epilithonimonas caeni	100.0	1363	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	97.72	97.72	0.84	0.84	2	conclusive
GCF_900102265.1	s__Epilithonimonas hungarica	90.3703	1067	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	97.55	97.55	0.87	0.87	2	-
GCA_003248755.1	s__Epilithonimonas sp003248755	87.9085	826	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385395.1	s__Epilithonimonas hispanica	84.115	740	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141765.1	s__Epilithonimonas zeae	83.929	870	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610695.1	s__Epilithonimonas arachidiradicis	83.7491	828	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002345565.1	s__Epilithonimonas sp002345565	83.5353	686	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860525.1	s__Epilithonimonas vandammei	82.3942	626	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	96.28	95.86	0.86	0.84	4	-
GCF_004365655.1	s__Epilithonimonas xixisoli	81.1909	681	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001643375.1	s__Epilithonimonas sp001643375	80.8565	683	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:44,369] [INFO] GTDB search result was written to GCF_000426465.1_ASM42646v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:44,369] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:44,371] [INFO] DFAST_QC result json was written to GCF_000426465.1_ASM42646v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:44,372] [INFO] DFAST_QC completed!
[2024-01-24 13:38:44,372] [INFO] Total running time: 0h1m19s