[2024-01-24 13:25:31,175] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,177] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a1f1abd-3e65-4200-89a0-b3b5490e4c15/dqc_reference
[2024-01-24 13:25:32,591] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,592] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,593] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3fb5549-e9f1-49d6-88f6-7f3829e87973/GCF_001005305.1_ASM100530v1_genomic.fna.gz | prodigal -d GCF_001005305.1_ASM100530v1_genomic.fna/cds.fna -a GCF_001005305.1_ASM100530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:48,444] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:48,444] [INFO] Task started: HMMsearch
[2024-01-24 13:25:48,444] [INFO] Running command: hmmsearch --tblout GCF_001005305.1_ASM100530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a1f1abd-3e65-4200-89a0-b3b5490e4c15/dqc_reference/reference_markers.hmm GCF_001005305.1_ASM100530v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:48,730] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:48,732] [INFO] Found 6/6 markers.
[2024-01-24 13:25:48,774] [INFO] Query marker FASTA was written to GCF_001005305.1_ASM100530v1_genomic.fna/markers.fasta
[2024-01-24 13:25:48,775] [INFO] Task started: Blastn
[2024-01-24 13:25:48,775] [INFO] Running command: blastn -query GCF_001005305.1_ASM100530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a1f1abd-3e65-4200-89a0-b3b5490e4c15/dqc_reference/reference_markers.fasta -out GCF_001005305.1_ASM100530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:49,504] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:49,508] [INFO] Selected 12 target genomes.
[2024-01-24 13:25:49,508] [INFO] Target genome list was writen to GCF_001005305.1_ASM100530v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:49,517] [INFO] Task started: fastANI
[2024-01-24 13:25:49,518] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3fb5549-e9f1-49d6-88f6-7f3829e87973/GCF_001005305.1_ASM100530v1_genomic.fna.gz --refList GCF_001005305.1_ASM100530v1_genomic.fna/target_genomes.txt --output GCF_001005305.1_ASM100530v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:59,129] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:59,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a1f1abd-3e65-4200-89a0-b3b5490e4c15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:59,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a1f1abd-3e65-4200-89a0-b3b5490e4c15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:59,140] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:59,140] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:59,141] [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
Kordia zhangzhouensis	strain=MCCC 1A00726	GCA_001005305.1	1620405	1620405	type	True	100.0	1323	1324	95	conclusive
Kordia periserrulae	strain=DSM 25731	GCA_003054265.1	701523	701523	type	True	79.6781	662	1324	95	below_threshold
Kordia algicida	strain=OT-1	GCA_000154725.1	221066	221066	type	True	79.5741	762	1324	95	below_threshold
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	79.2318	636	1324	95	below_threshold
Kordia aestuariivivens	strain=YSTF-M3	GCA_014397005.1	2759037	2759037	type	True	79.015	679	1324	95	below_threshold
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	78.8201	629	1324	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.685	117	1324	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.4397	106	1324	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	76.399	77	1324	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.3362	101	1324	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.1844	146	1324	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.1119	122	1324	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:59,142] [INFO] DFAST Taxonomy check result was written to GCF_001005305.1_ASM100530v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:59,143] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:59,143] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:59,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a1f1abd-3e65-4200-89a0-b3b5490e4c15/dqc_reference/checkm_data
[2024-01-24 13:25:59,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:59,184] [INFO] Task started: CheckM
[2024-01-24 13:25:59,185] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001005305.1_ASM100530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001005305.1_ASM100530v1_genomic.fna/checkm_input GCF_001005305.1_ASM100530v1_genomic.fna/checkm_result
[2024-01-24 13:26:45,782] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:45,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:45,806] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:45,806] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:45,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001005305.1_ASM100530v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:45,807] [INFO] Task started: Blastn
[2024-01-24 13:26:45,807] [INFO] Running command: blastn -query GCF_001005305.1_ASM100530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a1f1abd-3e65-4200-89a0-b3b5490e4c15/dqc_reference/reference_markers_gtdb.fasta -out GCF_001005305.1_ASM100530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:46,653] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:46,657] [INFO] Selected 8 target genomes.
[2024-01-24 13:26:46,657] [INFO] Target genome list was writen to GCF_001005305.1_ASM100530v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:46,665] [INFO] Task started: fastANI
[2024-01-24 13:26:46,665] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3fb5549-e9f1-49d6-88f6-7f3829e87973/GCF_001005305.1_ASM100530v1_genomic.fna.gz --refList GCF_001005305.1_ASM100530v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001005305.1_ASM100530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:54,898] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:54,910] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:54,910] [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_001005305.1	s__Kordia zhangzhouensis	100.0	1323	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003054265.1	s__Kordia periserrulae	79.662	664	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006383075.2	s__Kordia sp006383075	79.6019	692	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154725.1	s__Kordia algicida	79.5741	762	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005315.1	s__Kordia jejudonensis	79.2246	637	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352465.1	s__Kordia sp003352465	79.1173	675	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397005.1	s__Kordia aestuariivivens	79.0081	680	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009901525.1	s__Kordia antarctica	78.8412	626	1324	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:54,912] [INFO] GTDB search result was written to GCF_001005305.1_ASM100530v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:54,913] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:54,916] [INFO] DFAST_QC result json was written to GCF_001005305.1_ASM100530v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:54,917] [INFO] DFAST_QC completed!
[2024-01-24 13:26:54,917] [INFO] Total running time: 0h1m24s