[2024-01-24 13:09:49,887] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,889] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,889] [INFO] DQC Reference Directory: /var/lib/cwl/stgc55cb606-f778-4196-adf5-70b190c5930e/dqc_reference
[2024-01-24 13:09:51,159] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:51,162] [INFO] Task started: Prodigal
[2024-01-24 13:09:51,164] [INFO] Running command: gunzip -c /var/lib/cwl/stg60144a70-9e79-42ad-92ad-b0dcd20ad5a7/GCF_000695255.1_Phalotolerans2753_genomic.fna.gz | prodigal -d GCF_000695255.1_Phalotolerans2753_genomic.fna/cds.fna -a GCF_000695255.1_Phalotolerans2753_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:05,260] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:05,260] [INFO] Task started: HMMsearch
[2024-01-24 13:10:05,261] [INFO] Running command: hmmsearch --tblout GCF_000695255.1_Phalotolerans2753_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc55cb606-f778-4196-adf5-70b190c5930e/dqc_reference/reference_markers.hmm GCF_000695255.1_Phalotolerans2753_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:05,553] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:05,554] [INFO] Found 6/6 markers.
[2024-01-24 13:10:05,598] [INFO] Query marker FASTA was written to GCF_000695255.1_Phalotolerans2753_genomic.fna/markers.fasta
[2024-01-24 13:10:05,599] [INFO] Task started: Blastn
[2024-01-24 13:10:05,599] [INFO] Running command: blastn -query GCF_000695255.1_Phalotolerans2753_genomic.fna/markers.fasta -db /var/lib/cwl/stgc55cb606-f778-4196-adf5-70b190c5930e/dqc_reference/reference_markers.fasta -out GCF_000695255.1_Phalotolerans2753_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:06,252] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:06,255] [INFO] Selected 15 target genomes.
[2024-01-24 13:10:06,256] [INFO] Target genome list was writen to GCF_000695255.1_Phalotolerans2753_genomic.fna/target_genomes.txt
[2024-01-24 13:10:06,260] [INFO] Task started: fastANI
[2024-01-24 13:10:06,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg60144a70-9e79-42ad-92ad-b0dcd20ad5a7/GCF_000695255.1_Phalotolerans2753_genomic.fna.gz --refList GCF_000695255.1_Phalotolerans2753_genomic.fna/target_genomes.txt --output GCF_000695255.1_Phalotolerans2753_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:16,780] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:16,781] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc55cb606-f778-4196-adf5-70b190c5930e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:16,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc55cb606-f778-4196-adf5-70b190c5930e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:16,790] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:16,790] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:16,791] [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
Photobacterium galatheae	strain=S2753	GCA_000695255.1	1654360	1654360	type	True	100.0	1472	1480	95	conclusive
Photobacterium galatheae	strain=DSM 100496	GCA_023653475.1	1654360	1654360	type	True	99.9915	1472	1480	95	conclusive
Photobacterium arenosum	strain=CAU 1568	GCA_014841115.1	2774143	2774143	type	True	81.8489	709	1480	95	below_threshold
Photobacterium halotolerans	strain=DSM 18316	GCA_000425165.1	265726	265726	type	True	81.5609	729	1480	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	81.5169	732	1480	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	78.0532	120	1480	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	77.959	111	1480	95	below_threshold
Vibrio albus	strain=E4404	GCA_003144035.1	2200953	2200953	type	True	77.6086	134	1480	95	below_threshold
Vibrio fujianensis	strain=FJ201301	GCA_002749895.1	1974215	1974215	type	True	77.5755	69	1480	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:16,792] [INFO] DFAST Taxonomy check result was written to GCF_000695255.1_Phalotolerans2753_genomic.fna/tc_result.tsv
[2024-01-24 13:10:16,792] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:16,793] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:16,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc55cb606-f778-4196-adf5-70b190c5930e/dqc_reference/checkm_data
[2024-01-24 13:10:16,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:16,841] [INFO] Task started: CheckM
[2024-01-24 13:10:16,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000695255.1_Phalotolerans2753_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000695255.1_Phalotolerans2753_genomic.fna/checkm_input GCF_000695255.1_Phalotolerans2753_genomic.fna/checkm_result
[2024-01-24 13:11:02,489] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:02,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:02,510] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:02,511] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:02,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000695255.1_Phalotolerans2753_genomic.fna/markers.fasta)
[2024-01-24 13:11:02,511] [INFO] Task started: Blastn
[2024-01-24 13:11:02,512] [INFO] Running command: blastn -query GCF_000695255.1_Phalotolerans2753_genomic.fna/markers.fasta -db /var/lib/cwl/stgc55cb606-f778-4196-adf5-70b190c5930e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000695255.1_Phalotolerans2753_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:03,336] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:03,340] [INFO] Selected 15 target genomes.
[2024-01-24 13:11:03,340] [INFO] Target genome list was writen to GCF_000695255.1_Phalotolerans2753_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:03,350] [INFO] Task started: fastANI
[2024-01-24 13:11:03,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg60144a70-9e79-42ad-92ad-b0dcd20ad5a7/GCF_000695255.1_Phalotolerans2753_genomic.fna.gz --refList GCF_000695255.1_Phalotolerans2753_genomic.fna/target_genomes_gtdb.txt --output GCF_000695255.1_Phalotolerans2753_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:13,664] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:13,676] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:13,676] [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_000695255.1	s__Photobacterium galatheae	100.0	1472	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018199995.1	s__Photobacterium sp018199995	82.3028	834	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841115.1	s__Photobacterium sp014841115	81.8489	709	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.86	98.86	0.94	0.94	2	-
GCF_000972145.1	s__Photobacterium halotolerans_A	81.5781	723	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425165.1	s__Photobacterium halotolerans	81.5664	728	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.98	97.78	0.94	0.93	4	-
GCF_003614885.1	s__Photobacterium sp003614885	81.5263	731	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002196515.1	s__Vibrio gazogenes_A	77.6255	76	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860525.1	s__Vibrio hepatarius_B	77.6012	72	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:13,678] [INFO] GTDB search result was written to GCF_000695255.1_Phalotolerans2753_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:13,678] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:13,681] [INFO] DFAST_QC result json was written to GCF_000695255.1_Phalotolerans2753_genomic.fna/dqc_result.json
[2024-01-24 13:11:13,681] [INFO] DFAST_QC completed!
[2024-01-24 13:11:13,682] [INFO] Total running time: 0h1m24s