[2024-01-24 13:57:55,866] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:55,878] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:55,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b5357e5-db5f-4c39-969f-fcf97de18420/dqc_reference
[2024-01-24 13:57:57,296] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,297] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,297] [INFO] Running command: gunzip -c /var/lib/cwl/stg78eb935c-e4d6-4581-bdff-3c4422cffc44/GCF_002806995.1_ASM280699v1_genomic.fna.gz | prodigal -d GCF_002806995.1_ASM280699v1_genomic.fna/cds.fna -a GCF_002806995.1_ASM280699v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:11,449] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:11,450] [INFO] Task started: HMMsearch
[2024-01-24 13:58:11,450] [INFO] Running command: hmmsearch --tblout GCF_002806995.1_ASM280699v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b5357e5-db5f-4c39-969f-fcf97de18420/dqc_reference/reference_markers.hmm GCF_002806995.1_ASM280699v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:11,749] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:11,751] [INFO] Found 6/6 markers.
[2024-01-24 13:58:11,786] [INFO] Query marker FASTA was written to GCF_002806995.1_ASM280699v1_genomic.fna/markers.fasta
[2024-01-24 13:58:11,786] [INFO] Task started: Blastn
[2024-01-24 13:58:11,787] [INFO] Running command: blastn -query GCF_002806995.1_ASM280699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b5357e5-db5f-4c39-969f-fcf97de18420/dqc_reference/reference_markers.fasta -out GCF_002806995.1_ASM280699v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:12,527] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:12,530] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:12,530] [INFO] Target genome list was writen to GCF_002806995.1_ASM280699v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:12,535] [INFO] Task started: fastANI
[2024-01-24 13:58:12,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg78eb935c-e4d6-4581-bdff-3c4422cffc44/GCF_002806995.1_ASM280699v1_genomic.fna.gz --refList GCF_002806995.1_ASM280699v1_genomic.fna/target_genomes.txt --output GCF_002806995.1_ASM280699v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:22,717] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:22,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b5357e5-db5f-4c39-969f-fcf97de18420/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:22,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b5357e5-db5f-4c39-969f-fcf97de18420/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:22,738] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:22,738] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:22,738] [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
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	100.0	1101	1102	95	conclusive
Confluentibacter citreus	strain=XJNY	GCA_002807055.1	2007307	2007307	type	True	87.6714	911	1102	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	86.2126	883	1102	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	81.8698	713	1102	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	79.0793	419	1102	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	79.0044	432	1102	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	77.82	302	1102	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.7028	281	1102	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.4729	198	1102	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.4246	232	1102	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.3851	241	1102	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.0893	199	1102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:22,740] [INFO] DFAST Taxonomy check result was written to GCF_002806995.1_ASM280699v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:22,741] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:22,741] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:22,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b5357e5-db5f-4c39-969f-fcf97de18420/dqc_reference/checkm_data
[2024-01-24 13:58:22,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:22,781] [INFO] Task started: CheckM
[2024-01-24 13:58:22,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002806995.1_ASM280699v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002806995.1_ASM280699v1_genomic.fna/checkm_input GCF_002806995.1_ASM280699v1_genomic.fna/checkm_result
[2024-01-24 13:59:03,629] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:03,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:03,652] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:03,652] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:03,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002806995.1_ASM280699v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:03,653] [INFO] Task started: Blastn
[2024-01-24 13:59:03,654] [INFO] Running command: blastn -query GCF_002806995.1_ASM280699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b5357e5-db5f-4c39-969f-fcf97de18420/dqc_reference/reference_markers_gtdb.fasta -out GCF_002806995.1_ASM280699v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:04,626] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:04,630] [INFO] Selected 8 target genomes.
[2024-01-24 13:59:04,630] [INFO] Target genome list was writen to GCF_002806995.1_ASM280699v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:04,644] [INFO] Task started: fastANI
[2024-01-24 13:59:04,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg78eb935c-e4d6-4581-bdff-3c4422cffc44/GCF_002806995.1_ASM280699v1_genomic.fna.gz --refList GCF_002806995.1_ASM280699v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002806995.1_ASM280699v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:10,775] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:10,783] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:10,783] [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_002806995.1	s__Confluentibacter lentus	100.0	1101	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002280395.1	s__Confluentibacter sp002280395	90.0633	509	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807055.1	s__Confluentibacter citreus	87.6714	911	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843175.1	s__Confluentibacter flavum	86.1997	884	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258355.1	s__Confluentibacter sp003258355	81.8698	713	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814435.1	s__Mariniflexile gromovii	79.0739	420	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002784145.1	s__Yeosuana sp002784145	78.3276	312	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCF_900114265.1	s__Flaviramulus basaltis	78.3199	404	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:10,784] [INFO] GTDB search result was written to GCF_002806995.1_ASM280699v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:10,785] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:10,788] [INFO] DFAST_QC result json was written to GCF_002806995.1_ASM280699v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:10,788] [INFO] DFAST_QC completed!
[2024-01-24 13:59:10,788] [INFO] Total running time: 0h1m15s