[2024-01-24 13:46:01,514] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,516] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ed3c25c-f369-4c31-a5d8-0eaa272edfb2/dqc_reference
[2024-01-24 13:46:02,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,778] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,778] [INFO] Running command: gunzip -c /var/lib/cwl/stg0561c26f-1632-458e-b0c1-6c03c6f5903a/GCF_014397005.1_ASM1439700v1_genomic.fna.gz | prodigal -d GCF_014397005.1_ASM1439700v1_genomic.fna/cds.fna -a GCF_014397005.1_ASM1439700v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:23,840] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:23,840] [INFO] Task started: HMMsearch
[2024-01-24 13:46:23,841] [INFO] Running command: hmmsearch --tblout GCF_014397005.1_ASM1439700v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ed3c25c-f369-4c31-a5d8-0eaa272edfb2/dqc_reference/reference_markers.hmm GCF_014397005.1_ASM1439700v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:24,188] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:24,189] [INFO] Found 6/6 markers.
[2024-01-24 13:46:24,240] [INFO] Query marker FASTA was written to GCF_014397005.1_ASM1439700v1_genomic.fna/markers.fasta
[2024-01-24 13:46:24,240] [INFO] Task started: Blastn
[2024-01-24 13:46:24,240] [INFO] Running command: blastn -query GCF_014397005.1_ASM1439700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ed3c25c-f369-4c31-a5d8-0eaa272edfb2/dqc_reference/reference_markers.fasta -out GCF_014397005.1_ASM1439700v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:24,976] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:24,984] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:24,985] [INFO] Target genome list was writen to GCF_014397005.1_ASM1439700v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:25,005] [INFO] Task started: fastANI
[2024-01-24 13:46:25,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg0561c26f-1632-458e-b0c1-6c03c6f5903a/GCF_014397005.1_ASM1439700v1_genomic.fna.gz --refList GCF_014397005.1_ASM1439700v1_genomic.fna/target_genomes.txt --output GCF_014397005.1_ASM1439700v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:35,588] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:35,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ed3c25c-f369-4c31-a5d8-0eaa272edfb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:35,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ed3c25c-f369-4c31-a5d8-0eaa272edfb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:35,598] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:35,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:35,598] [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 aestuariivivens	strain=YSTF-M3	GCA_014397005.1	2759037	2759037	type	True	100.0	1802	1804	95	conclusive
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	83.7123	1141	1804	95	below_threshold
Kordia algicida	strain=OT-1	GCA_000154725.1	221066	221066	type	True	81.5462	1027	1804	95	below_threshold
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	81.4978	971	1804	95	below_threshold
Kordia periserrulae	strain=DSM 25731	GCA_003054265.1	701523	701523	type	True	79.7005	875	1804	95	below_threshold
Kordia zhangzhouensis	strain=MCCC 1A00726	GCA_001005305.1	1620405	1620405	type	True	78.929	667	1804	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.0761	125	1804	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.7194	161	1804	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.5671	116	1804	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.5386	161	1804	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.5018	145	1804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:35,600] [INFO] DFAST Taxonomy check result was written to GCF_014397005.1_ASM1439700v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:35,601] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:35,601] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:35,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ed3c25c-f369-4c31-a5d8-0eaa272edfb2/dqc_reference/checkm_data
[2024-01-24 13:46:35,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:35,657] [INFO] Task started: CheckM
[2024-01-24 13:46:35,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014397005.1_ASM1439700v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014397005.1_ASM1439700v1_genomic.fna/checkm_input GCF_014397005.1_ASM1439700v1_genomic.fna/checkm_result
[2024-01-24 13:47:37,522] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:37,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:37,544] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:37,545] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:37,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014397005.1_ASM1439700v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:37,545] [INFO] Task started: Blastn
[2024-01-24 13:47:37,546] [INFO] Running command: blastn -query GCF_014397005.1_ASM1439700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ed3c25c-f369-4c31-a5d8-0eaa272edfb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014397005.1_ASM1439700v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:38,469] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:38,472] [INFO] Selected 6 target genomes.
[2024-01-24 13:47:38,472] [INFO] Target genome list was writen to GCF_014397005.1_ASM1439700v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:38,475] [INFO] Task started: fastANI
[2024-01-24 13:47:38,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg0561c26f-1632-458e-b0c1-6c03c6f5903a/GCF_014397005.1_ASM1439700v1_genomic.fna.gz --refList GCF_014397005.1_ASM1439700v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014397005.1_ASM1439700v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:47,268] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:47,281] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:47,281] [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_014397005.1	s__Kordia aestuariivivens	100.0	1802	1804	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_009901525.1	s__Kordia antarctica	83.6492	1150	1804	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	81.5511	1028	1804	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	81.4939	974	1804	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	80.4687	988	1804	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054265.1	s__Kordia periserrulae	79.7026	875	1804	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 13:47:47,283] [INFO] GTDB search result was written to GCF_014397005.1_ASM1439700v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:47,283] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:47,286] [INFO] DFAST_QC result json was written to GCF_014397005.1_ASM1439700v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:47,286] [INFO] DFAST_QC completed!
[2024-01-24 13:47:47,286] [INFO] Total running time: 0h1m46s