[2024-01-24 14:47:27,074] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:27,076] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:27,077] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1e5ec06-9994-4eba-a0c7-802e33619ec1/dqc_reference
[2024-01-24 14:47:28,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:28,488] [INFO] Task started: Prodigal
[2024-01-24 14:47:28,488] [INFO] Running command: gunzip -c /var/lib/cwl/stg3602da6e-891e-4dd3-81fc-b0190a27c26f/GCF_004115975.1_ASM411597v1_genomic.fna.gz | prodigal -d GCF_004115975.1_ASM411597v1_genomic.fna/cds.fna -a GCF_004115975.1_ASM411597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:49,312] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:49,312] [INFO] Task started: HMMsearch
[2024-01-24 14:47:49,312] [INFO] Running command: hmmsearch --tblout GCF_004115975.1_ASM411597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1e5ec06-9994-4eba-a0c7-802e33619ec1/dqc_reference/reference_markers.hmm GCF_004115975.1_ASM411597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:49,632] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:49,634] [INFO] Found 6/6 markers.
[2024-01-24 14:47:49,690] [INFO] Query marker FASTA was written to GCF_004115975.1_ASM411597v1_genomic.fna/markers.fasta
[2024-01-24 14:47:49,690] [INFO] Task started: Blastn
[2024-01-24 14:47:49,690] [INFO] Running command: blastn -query GCF_004115975.1_ASM411597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1e5ec06-9994-4eba-a0c7-802e33619ec1/dqc_reference/reference_markers.fasta -out GCF_004115975.1_ASM411597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:50,395] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:50,399] [INFO] Selected 15 target genomes.
[2024-01-24 14:47:50,400] [INFO] Target genome list was writen to GCF_004115975.1_ASM411597v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:50,416] [INFO] Task started: fastANI
[2024-01-24 14:47:50,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg3602da6e-891e-4dd3-81fc-b0190a27c26f/GCF_004115975.1_ASM411597v1_genomic.fna.gz --refList GCF_004115975.1_ASM411597v1_genomic.fna/target_genomes.txt --output GCF_004115975.1_ASM411597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:02,703] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:02,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1e5ec06-9994-4eba-a0c7-802e33619ec1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:02,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1e5ec06-9994-4eba-a0c7-802e33619ec1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:02,717] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:02,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:02,717] [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 gilvus	strain=IC158	GCA_004115975.1	59602	59602	type	True	100.0	1522	1522	95	conclusive
Gelidibacter pelagius	strain=DF109	GCA_017581925.1	2819985	2819985	type	True	85.8367	1090	1522	95	below_threshold
Gelidibacter japonicus	strain=Bio7-1	GCA_010725055.1	1962232	1962232	type	True	83.605	1038	1522	95	below_threshold
Gelidibacter maritimus	strain=F6074	GCA_014062315.1	2761487	2761487	type	True	82.5075	998	1522	95	below_threshold
Gelidibacter mesophilus	strain=DSM 14095	GCA_000423005.1	169050	169050	type	True	80.8877	870	1522	95	below_threshold
Gelidibacter algens	strain=DSM 12408	GCA_003259265.1	49280	49280	type	True	79.7786	682	1522	95	below_threshold
Gelidibacter algens	strain=ACAM 536	GCA_001678675.1	49280	49280	type	True	79.6988	667	1522	95	below_threshold
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	78.9733	521	1522	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	77.0672	135	1522	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.9192	189	1522	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.8984	143	1522	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.7856	69	1522	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.5015	135	1522	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.2731	73	1522	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.1824	74	1522	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:02,719] [INFO] DFAST Taxonomy check result was written to GCF_004115975.1_ASM411597v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:02,720] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:02,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:02,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1e5ec06-9994-4eba-a0c7-802e33619ec1/dqc_reference/checkm_data
[2024-01-24 14:48:02,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:02,770] [INFO] Task started: CheckM
[2024-01-24 14:48:02,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004115975.1_ASM411597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004115975.1_ASM411597v1_genomic.fna/checkm_input GCF_004115975.1_ASM411597v1_genomic.fna/checkm_result
[2024-01-24 14:49:02,425] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:02,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:02,442] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:02,442] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:02,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004115975.1_ASM411597v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:02,443] [INFO] Task started: Blastn
[2024-01-24 14:49:02,443] [INFO] Running command: blastn -query GCF_004115975.1_ASM411597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1e5ec06-9994-4eba-a0c7-802e33619ec1/dqc_reference/reference_markers_gtdb.fasta -out GCF_004115975.1_ASM411597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:03,493] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:03,497] [INFO] Selected 9 target genomes.
[2024-01-24 14:49:03,497] [INFO] Target genome list was writen to GCF_004115975.1_ASM411597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:03,515] [INFO] Task started: fastANI
[2024-01-24 14:49:03,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg3602da6e-891e-4dd3-81fc-b0190a27c26f/GCF_004115975.1_ASM411597v1_genomic.fna.gz --refList GCF_004115975.1_ASM411597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004115975.1_ASM411597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:14,076] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:14,086] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:14,087] [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_004115975.1	s__Gelidibacter gilvus	100.0	1522	1522	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_017581925.1	s__Gelidibacter sp017581925	85.8407	1090	1522	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	83.6097	1037	1522	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	82.5008	998	1522	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423005.1	s__Gelidibacter mesophilus	80.8877	870	1522	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	79.706	666	1522	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	99.95	99.95	0.98	0.98	2	-
GCF_016469035.1	s__Gelidibacter salicanalis_A	79.4777	687	1522	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	77.6355	219	1522	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.2886	193	1522	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:14,089] [INFO] GTDB search result was written to GCF_004115975.1_ASM411597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:14,090] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:14,095] [INFO] DFAST_QC result json was written to GCF_004115975.1_ASM411597v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:14,096] [INFO] DFAST_QC completed!
[2024-01-24 14:49:14,096] [INFO] Total running time: 0h1m47s