[2024-01-24 12:48:20,531] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:48:20,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:48:20,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fd2a644-779a-4d64-ac86-2418cadbcdcf/dqc_reference
[2024-01-24 12:48:21,767] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:48:21,768] [INFO] Task started: Prodigal
[2024-01-24 12:48:21,769] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc0e1b78-1622-455b-bb47-62389b3d2e08/GCF_030409905.1_ASM3040990v1_genomic.fna.gz | prodigal -d GCF_030409905.1_ASM3040990v1_genomic.fna/cds.fna -a GCF_030409905.1_ASM3040990v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:43,345] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:43,345] [INFO] Task started: HMMsearch
[2024-01-24 12:48:43,346] [INFO] Running command: hmmsearch --tblout GCF_030409905.1_ASM3040990v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fd2a644-779a-4d64-ac86-2418cadbcdcf/dqc_reference/reference_markers.hmm GCF_030409905.1_ASM3040990v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:43,619] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:43,621] [INFO] Found 6/6 markers.
[2024-01-24 12:48:43,660] [INFO] Query marker FASTA was written to GCF_030409905.1_ASM3040990v1_genomic.fna/markers.fasta
[2024-01-24 12:48:43,660] [INFO] Task started: Blastn
[2024-01-24 12:48:43,660] [INFO] Running command: blastn -query GCF_030409905.1_ASM3040990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fd2a644-779a-4d64-ac86-2418cadbcdcf/dqc_reference/reference_markers.fasta -out GCF_030409905.1_ASM3040990v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:44,257] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:44,261] [INFO] Selected 26 target genomes.
[2024-01-24 12:48:44,262] [INFO] Target genome list was writen to GCF_030409905.1_ASM3040990v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:44,282] [INFO] Task started: fastANI
[2024-01-24 12:48:44,283] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc0e1b78-1622-455b-bb47-62389b3d2e08/GCF_030409905.1_ASM3040990v1_genomic.fna.gz --refList GCF_030409905.1_ASM3040990v1_genomic.fna/target_genomes.txt --output GCF_030409905.1_ASM3040990v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:49:06,887] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:06,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fd2a644-779a-4d64-ac86-2418cadbcdcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:49:06,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fd2a644-779a-4d64-ac86-2418cadbcdcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:49:06,914] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:49:06,914] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:49:06,915] [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
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	77.9443	318	1507	95	below_threshold
Echinicola arenosa	strain=CAU 1574	GCA_014841125.1	2774144	2774144	type	True	77.6828	293	1507	95	below_threshold
Echinicola soli	strain=LN3S3	GCA_006575665.1	2591634	2591634	type	True	77.6743	258	1507	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	77.6604	308	1507	95	below_threshold
Litoribacter populi	strain=XAAS-A1	GCA_007483685.1	2598460	2598460	type	True	77.6491	119	1507	95	below_threshold
Echinicola rosea	strain=JL3085	GCA_005281475.1	1807691	1807691	type	True	77.6469	251	1507	95	below_threshold
Echinicola shivajiensis	strain=AK12	GCA_018642165.1	1035916	1035916	type	True	77.6399	308	1507	95	below_threshold
Echinicola strongylocentroti	strain=MEBiC08714	GCA_003260975.1	1795355	1795355	type	True	77.5916	274	1507	95	below_threshold
Echinicola rosea	strain=CGMCC 1.15407	GCA_014642715.1	1807691	1807691	type	True	77.4797	249	1507	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	77.1348	86	1507	95	below_threshold
Aquiflexum balticum	strain=DSM 16537	GCA_900176595.1	280473	280473	type	True	77.0264	129	1507	95	below_threshold
Echinicola pacifica	strain=KCTC 12368	GCA_014651455.1	346377	346377	type	True	76.9721	193	1507	95	below_threshold
Echinicola pacifica	strain=DSM 19836	GCA_000373245.1	346377	346377	type	True	76.9513	192	1507	95	below_threshold
Cyclobacterium amurskyense	strain=KCTC 12363	GCA_001050135.1	320787	320787	type	True	76.8111	105	1507	95	below_threshold
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	76.5356	82	1507	95	below_threshold
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	76.4277	117	1507	95	below_threshold
Algoriphagus resistens	strain=NH1	GCA_001442615.1	1750590	1750590	type	True	76.3442	69	1507	95	below_threshold
Pleomorphovibrio marinus	strain=SW125	GCA_003347495.1	2164132	2164132	type	True	76.2973	94	1507	95	below_threshold
Lunatibacter salilacus	strain=CUG 91308	GCA_009797935.1	2483804	2483804	type	True	76.1482	87	1507	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	76.0855	73	1507	95	below_threshold
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	75.911	93	1507	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	75.6487	69	1507	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:49:06,916] [INFO] DFAST Taxonomy check result was written to GCF_030409905.1_ASM3040990v1_genomic.fna/tc_result.tsv
[2024-01-24 12:49:06,917] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:49:06,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:49:06,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fd2a644-779a-4d64-ac86-2418cadbcdcf/dqc_reference/checkm_data
[2024-01-24 12:49:06,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:49:06,965] [INFO] Task started: CheckM
[2024-01-24 12:49:06,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409905.1_ASM3040990v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409905.1_ASM3040990v1_genomic.fna/checkm_input GCF_030409905.1_ASM3040990v1_genomic.fna/checkm_result
[2024-01-24 12:50:08,123] [INFO] Task succeeded: CheckM
[2024-01-24 12:50:08,124] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:50:08,149] [INFO] ===== Completeness check finished =====
[2024-01-24 12:50:08,149] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:50:08,150] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409905.1_ASM3040990v1_genomic.fna/markers.fasta)
[2024-01-24 12:50:08,150] [INFO] Task started: Blastn
[2024-01-24 12:50:08,150] [INFO] Running command: blastn -query GCF_030409905.1_ASM3040990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fd2a644-779a-4d64-ac86-2418cadbcdcf/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409905.1_ASM3040990v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:50:08,950] [INFO] Task succeeded: Blastn
[2024-01-24 12:50:08,955] [INFO] Selected 30 target genomes.
[2024-01-24 12:50:08,955] [INFO] Target genome list was writen to GCF_030409905.1_ASM3040990v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:50:08,996] [INFO] Task started: fastANI
[2024-01-24 12:50:08,997] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc0e1b78-1622-455b-bb47-62389b3d2e08/GCF_030409905.1_ASM3040990v1_genomic.fna.gz --refList GCF_030409905.1_ASM3040990v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409905.1_ASM3040990v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:50:32,428] [INFO] Task succeeded: fastANI
[2024-01-24 12:50:32,449] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:50:32,450] [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_015533855.1	s__Echinicola sp015533855	78.0497	297	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006575665.1	s__Echinicola sp006575665	77.7826	260	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281475.1	s__Echinicola rosea	77.6979	250	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018642165.1	s__Echinicola shivajiensis	77.6975	308	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841125.1	s__Echinicola sp014841125	77.6936	292	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280965.1	s__Echinicola sp014280965	77.6601	308	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007483685.1	s__Litoribacter sp007483685	77.5997	119	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260975.1	s__Echinicola strongylocentroti	77.5741	272	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018500185.1	s__Litoribacter ruber	77.3227	107	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	98.60	98.60	0.91	0.91	2	-
GCF_900176595.1	s__Aquiflexum balticum	77.2604	131	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373245.1	s__Echinicola pacifica	76.9497	193	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001050135.1	s__Cyclobacterium amurskyense	76.8923	106	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000714815.1	s__Anditalea andensis	76.753	125	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Anditalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156785.1	s__Belliella pelovolcani	76.5325	95	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003005.1	s__Mongoliibacter ruber	76.5298	94	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295935.2	s__Indibacter alkaliphilus	76.4742	112	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476655.1	s__Aquiflexum lacus	76.4277	117	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442615.1	s__Algoriphagus resistens	76.3826	70	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347495.1	s__Negadavirga sp003347495	76.2794	95	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Negadavirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994275.1	s__Cyclobacterium jeungdonense	76.0582	77	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	76.0468	74	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119245.1	s__Cyclobacterium sp010119245	75.911	93	1507	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:50:32,452] [INFO] GTDB search result was written to GCF_030409905.1_ASM3040990v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:50:32,453] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:50:32,458] [INFO] DFAST_QC result json was written to GCF_030409905.1_ASM3040990v1_genomic.fna/dqc_result.json
[2024-01-24 12:50:32,459] [INFO] DFAST_QC completed!
[2024-01-24 12:50:32,459] [INFO] Total running time: 0h2m12s