[2024-01-24 13:32:56,681] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:56,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:56,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e3361df-1765-4737-be7b-a822c95f3b99/dqc_reference
[2024-01-24 13:32:57,936] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:57,937] [INFO] Task started: Prodigal
[2024-01-24 13:32:57,938] [INFO] Running command: gunzip -c /var/lib/cwl/stgc89c71be-9796-4d63-9b54-46563eb32d30/GCF_007997285.1_ASM799728v1_genomic.fna.gz | prodigal -d GCF_007997285.1_ASM799728v1_genomic.fna/cds.fna -a GCF_007997285.1_ASM799728v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:13,677] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:13,678] [INFO] Task started: HMMsearch
[2024-01-24 13:33:13,678] [INFO] Running command: hmmsearch --tblout GCF_007997285.1_ASM799728v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e3361df-1765-4737-be7b-a822c95f3b99/dqc_reference/reference_markers.hmm GCF_007997285.1_ASM799728v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:13,929] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:13,930] [INFO] Found 6/6 markers.
[2024-01-24 13:33:13,963] [INFO] Query marker FASTA was written to GCF_007997285.1_ASM799728v1_genomic.fna/markers.fasta
[2024-01-24 13:33:13,963] [INFO] Task started: Blastn
[2024-01-24 13:33:13,963] [INFO] Running command: blastn -query GCF_007997285.1_ASM799728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e3361df-1765-4737-be7b-a822c95f3b99/dqc_reference/reference_markers.fasta -out GCF_007997285.1_ASM799728v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:14,630] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:14,634] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:14,634] [INFO] Target genome list was writen to GCF_007997285.1_ASM799728v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:14,657] [INFO] Task started: fastANI
[2024-01-24 13:33:14,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgc89c71be-9796-4d63-9b54-46563eb32d30/GCF_007997285.1_ASM799728v1_genomic.fna.gz --refList GCF_007997285.1_ASM799728v1_genomic.fna/target_genomes.txt --output GCF_007997285.1_ASM799728v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:25,715] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:25,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e3361df-1765-4737-be7b-a822c95f3b99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:25,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e3361df-1765-4737-be7b-a822c95f3b99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:25,727] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:25,727] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:25,727] [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
Gelidibacter salicanalis	strain=IC162	GCA_007997285.1	291193	291193	type	True	100.0	1250	1251	95	conclusive
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	83.3101	791	1251	95	below_threshold
Gelidibacter algens	strain=DSM 12408	GCA_003259265.1	49280	49280	type	True	79.9184	597	1251	95	below_threshold
Gelidibacter algens	strain=ACAM 536	GCA_001678675.1	49280	49280	type	True	79.8735	590	1251	95	below_threshold
Gelidibacter mesophilus	strain=DSM 14095	GCA_000423005.1	169050	169050	type	True	78.9866	541	1251	95	below_threshold
Gelidibacter gilvus	strain=IC158	GCA_004115975.1	59602	59602	type	True	78.9827	573	1251	95	below_threshold
Gelidibacter pelagius	strain=DF109	GCA_017581925.1	2819985	2819985	type	True	78.9303	548	1251	95	below_threshold
Gelidibacter japonicus	strain=Bio7-1	GCA_010725055.1	1962232	1962232	type	True	78.7281	500	1251	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	77.0045	183	1251	95	below_threshold
Subsaximicrobium wynnwilliamsii	strain=G#7(T)	GCA_007997225.1	291179	291179	type	True	76.7423	177	1251	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.7359	108	1251	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	76.7191	166	1251	95	below_threshold
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	76.5115	87	1251	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.3039	68	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:25,728] [INFO] DFAST Taxonomy check result was written to GCF_007997285.1_ASM799728v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:25,729] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:25,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:25,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e3361df-1765-4737-be7b-a822c95f3b99/dqc_reference/checkm_data
[2024-01-24 13:33:25,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:25,772] [INFO] Task started: CheckM
[2024-01-24 13:33:25,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007997285.1_ASM799728v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007997285.1_ASM799728v1_genomic.fna/checkm_input GCF_007997285.1_ASM799728v1_genomic.fna/checkm_result
[2024-01-24 13:34:13,359] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:13,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:13,383] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:13,384] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:13,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007997285.1_ASM799728v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:13,384] [INFO] Task started: Blastn
[2024-01-24 13:34:13,385] [INFO] Running command: blastn -query GCF_007997285.1_ASM799728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e3361df-1765-4737-be7b-a822c95f3b99/dqc_reference/reference_markers_gtdb.fasta -out GCF_007997285.1_ASM799728v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:14,304] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:14,312] [INFO] Selected 12 target genomes.
[2024-01-24 13:34:14,312] [INFO] Target genome list was writen to GCF_007997285.1_ASM799728v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:14,322] [INFO] Task started: fastANI
[2024-01-24 13:34:14,322] [INFO] Running command: fastANI --query /var/lib/cwl/stgc89c71be-9796-4d63-9b54-46563eb32d30/GCF_007997285.1_ASM799728v1_genomic.fna.gz --refList GCF_007997285.1_ASM799728v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007997285.1_ASM799728v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:23,916] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:23,933] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:23,933] [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_007997285.1	s__Gelidibacter salicanalis	100.0	1250	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004364975.1	s__Gelidibacter sediminis	83.3101	791	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016469035.1	s__Gelidibacter salicanalis_A	82.6519	854	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678675.1	s__Gelidibacter algens	79.8598	592	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	99.95	99.95	0.98	0.98	2	-
GCF_000423005.1	s__Gelidibacter mesophilus	78.9866	541	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004115975.1	s__Gelidibacter gilvus	78.9862	572	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017581925.1	s__Gelidibacter sp017581925	78.9343	548	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010725055.1	s__Gelidibacter japonicus	78.7276	500	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014062315.1	s__Gelidibacter sp014062315	78.5021	503	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	76.9904	184	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403865.1	s__Winogradskyella costae	76.7191	166	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009495755.1	s__Flavobacterium sp009495755	76.0979	80	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:23,936] [INFO] GTDB search result was written to GCF_007997285.1_ASM799728v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:23,937] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:23,940] [INFO] DFAST_QC result json was written to GCF_007997285.1_ASM799728v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:23,940] [INFO] DFAST_QC completed!
[2024-01-24 13:34:23,940] [INFO] Total running time: 0h1m27s