[2024-01-25 19:09:05,959] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:05,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:05,961] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b3f726d-341f-4ea0-b374-2e9a51c56e25/dqc_reference
[2024-01-25 19:09:07,105] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:07,105] [INFO] Task started: Prodigal
[2024-01-25 19:09:07,106] [INFO] Running command: gunzip -c /var/lib/cwl/stgca4eaec4-b68c-44dc-8edf-00b368fbef8c/GCF_001995095.2_ASM199509v2_genomic.fna.gz | prodigal -d GCF_001995095.2_ASM199509v2_genomic.fna/cds.fna -a GCF_001995095.2_ASM199509v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:15,047] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:15,047] [INFO] Task started: HMMsearch
[2024-01-25 19:09:15,047] [INFO] Running command: hmmsearch --tblout GCF_001995095.2_ASM199509v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b3f726d-341f-4ea0-b374-2e9a51c56e25/dqc_reference/reference_markers.hmm GCF_001995095.2_ASM199509v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:15,284] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:15,285] [INFO] Found 6/6 markers.
[2024-01-25 19:09:15,314] [INFO] Query marker FASTA was written to GCF_001995095.2_ASM199509v2_genomic.fna/markers.fasta
[2024-01-25 19:09:15,314] [INFO] Task started: Blastn
[2024-01-25 19:09:15,314] [INFO] Running command: blastn -query GCF_001995095.2_ASM199509v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b3f726d-341f-4ea0-b374-2e9a51c56e25/dqc_reference/reference_markers.fasta -out GCF_001995095.2_ASM199509v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:16,019] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:16,021] [INFO] Selected 17 target genomes.
[2024-01-25 19:09:16,022] [INFO] Target genome list was writen to GCF_001995095.2_ASM199509v2_genomic.fna/target_genomes.txt
[2024-01-25 19:09:16,029] [INFO] Task started: fastANI
[2024-01-25 19:09:16,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgca4eaec4-b68c-44dc-8edf-00b368fbef8c/GCF_001995095.2_ASM199509v2_genomic.fna.gz --refList GCF_001995095.2_ASM199509v2_genomic.fna/target_genomes.txt --output GCF_001995095.2_ASM199509v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:29,255] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:29,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b3f726d-341f-4ea0-b374-2e9a51c56e25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:29,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b3f726d-341f-4ea0-b374-2e9a51c56e25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:29,264] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:09:29,264] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:29,264] [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
Oceanospirillum linum	strain=ATCC 11336	GCA_001995095.2	966	966	type	True	100.0	1211	1212	95	conclusive
Oceanospirillum sanctuarii	strain=AK56	GCA_002150805.1	1434821	1434821	type	True	81.7873	733	1212	95	below_threshold
Oceanospirillum maris	strain=DSM 6286	GCA_000422865.1	64977	64977	type	True	81.0062	516	1212	95	below_threshold
Oceanospirillum beijerinckii	strain=DSM 7166	GCA_000422425.1	64976	64976	type	True	78.9863	325	1212	95	below_threshold
Oceanospirillum multiglobuliferum	strain=ATCC 33336	GCA_002059185.1	64969	64969	type	True	78.0157	225	1212	95	below_threshold
Oceanospirillum multiglobuliferum	strain=ATCC 33336	GCA_900167095.1	64969	64969	type	True	77.9891	227	1212	95	below_threshold
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	76.8334	58	1212	95	below_threshold
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	76.597	64	1212	95	below_threshold
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	76.4634	81	1212	95	below_threshold
Amphritea opalescens	strain=ANRC-JH13	GCA_003957515.1	2490544	2490544	type	True	76.1823	62	1212	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:29,270] [INFO] DFAST Taxonomy check result was written to GCF_001995095.2_ASM199509v2_genomic.fna/tc_result.tsv
[2024-01-25 19:09:29,270] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:29,270] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:29,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b3f726d-341f-4ea0-b374-2e9a51c56e25/dqc_reference/checkm_data
[2024-01-25 19:09:29,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:29,318] [INFO] Task started: CheckM
[2024-01-25 19:09:29,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001995095.2_ASM199509v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001995095.2_ASM199509v2_genomic.fna/checkm_input GCF_001995095.2_ASM199509v2_genomic.fna/checkm_result
[2024-01-25 19:09:57,178] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:57,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.85%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:57,199] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:57,199] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:57,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001995095.2_ASM199509v2_genomic.fna/markers.fasta)
[2024-01-25 19:09:57,200] [INFO] Task started: Blastn
[2024-01-25 19:09:57,200] [INFO] Running command: blastn -query GCF_001995095.2_ASM199509v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b3f726d-341f-4ea0-b374-2e9a51c56e25/dqc_reference/reference_markers_gtdb.fasta -out GCF_001995095.2_ASM199509v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:58,347] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:58,350] [INFO] Selected 12 target genomes.
[2024-01-25 19:09:58,350] [INFO] Target genome list was writen to GCF_001995095.2_ASM199509v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:58,362] [INFO] Task started: fastANI
[2024-01-25 19:09:58,362] [INFO] Running command: fastANI --query /var/lib/cwl/stgca4eaec4-b68c-44dc-8edf-00b368fbef8c/GCF_001995095.2_ASM199509v2_genomic.fna.gz --refList GCF_001995095.2_ASM199509v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001995095.2_ASM199509v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:07,262] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:07,269] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:07,269] [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_001995095.2	s__Oceanospirillum linum	100.0	1211	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_002150805.1	s__Oceanospirillum sanctuarii	81.7877	733	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422865.1	s__Oceanospirillum maris	80.999	516	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422425.1	s__Oceanospirillum beijerinckii	78.9654	326	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	98.77	98.77	0.90	0.90	2	-
GCF_014164585.1	s__Oceanospirillum sp014164585	78.9286	294	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167095.1	s__Oceanospirillum multiglobuliferum	78.0072	228	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	99.98	99.98	0.99	0.99	2	-
GCF_017051665.1	s__Amphritea spongicola	76.449	83	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924235.1	s__Amphritea sp016924235	76.4417	71	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.30	99.30	0.95	0.95	2	-
GCF_003957515.1	s__Amphritea opalescens	76.1969	63	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:07,272] [INFO] GTDB search result was written to GCF_001995095.2_ASM199509v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:07,272] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:07,276] [INFO] DFAST_QC result json was written to GCF_001995095.2_ASM199509v2_genomic.fna/dqc_result.json
[2024-01-25 19:10:07,276] [INFO] DFAST_QC completed!
[2024-01-25 19:10:07,276] [INFO] Total running time: 0h1m1s