[2024-01-24 13:46:03,805] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:03,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:03,808] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc29cc66-7101-40a2-9484-491307b0f58a/dqc_reference
[2024-01-24 13:46:05,161] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:05,162] [INFO] Task started: Prodigal
[2024-01-24 13:46:05,162] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6cc420e-205d-45bc-9f61-9a26b0ba08ef/GCF_007989895.1_ASM798989v1_genomic.fna.gz | prodigal -d GCF_007989895.1_ASM798989v1_genomic.fna/cds.fna -a GCF_007989895.1_ASM798989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:16,182] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:16,182] [INFO] Task started: HMMsearch
[2024-01-24 13:46:16,182] [INFO] Running command: hmmsearch --tblout GCF_007989895.1_ASM798989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc29cc66-7101-40a2-9484-491307b0f58a/dqc_reference/reference_markers.hmm GCF_007989895.1_ASM798989v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:16,568] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:16,569] [INFO] Found 6/6 markers.
[2024-01-24 13:46:16,628] [INFO] Query marker FASTA was written to GCF_007989895.1_ASM798989v1_genomic.fna/markers.fasta
[2024-01-24 13:46:16,628] [INFO] Task started: Blastn
[2024-01-24 13:46:16,628] [INFO] Running command: blastn -query GCF_007989895.1_ASM798989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc29cc66-7101-40a2-9484-491307b0f58a/dqc_reference/reference_markers.fasta -out GCF_007989895.1_ASM798989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:17,457] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:17,463] [INFO] Selected 12 target genomes.
[2024-01-24 13:46:17,463] [INFO] Target genome list was writen to GCF_007989895.1_ASM798989v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:17,470] [INFO] Task started: fastANI
[2024-01-24 13:46:17,470] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6cc420e-205d-45bc-9f61-9a26b0ba08ef/GCF_007989895.1_ASM798989v1_genomic.fna.gz --refList GCF_007989895.1_ASM798989v1_genomic.fna/target_genomes.txt --output GCF_007989895.1_ASM798989v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:29,216] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:29,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc29cc66-7101-40a2-9484-491307b0f58a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:29,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc29cc66-7101-40a2-9484-491307b0f58a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:29,225] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:46:29,225] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:29,225] [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
Pseudoalteromonas peptidolytica	strain=NBRC 101021	GCA_007989895.1	61150	61150	type	True	100.0	1507	1518	95	conclusive
Pseudoalteromonas peptidolytica	strain=DSM 14001	GCA_012641745.1	61150	61150	type	True	99.9973	1518	1518	95	conclusive
Pseudoalteromonas peptidolytica	strain=F12-50-A1	GCA_014858745.1	61150	61150	type	True	99.997	1517	1518	95	conclusive
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	84.0392	922	1518	95	below_threshold
Pseudoalteromonas piscicida	strain=ATCC 15057	GCA_000382005.1	43662	43662	type	True	83.4403	918	1518	95	below_threshold
Pseudoalteromonas piscicida	strain=JCM 20779	GCA_000238315.4	43662	43662	type	True	83.3995	918	1518	95	below_threshold
Pseudoalteromonas flavipulchra	strain=NCIMB 2033	GCA_014858715.1	137779	137779	suspected-type	True	83.3983	937	1518	95	below_threshold
Pseudoalteromonas flavipulchra	strain=LMG 20361	GCA_014596995.1	137779	137779	suspected-type	True	83.3783	933	1518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:29,226] [INFO] DFAST Taxonomy check result was written to GCF_007989895.1_ASM798989v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:29,227] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:29,227] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:29,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc29cc66-7101-40a2-9484-491307b0f58a/dqc_reference/checkm_data
[2024-01-24 13:46:29,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:29,277] [INFO] Task started: CheckM
[2024-01-24 13:46:29,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989895.1_ASM798989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989895.1_ASM798989v1_genomic.fna/checkm_input GCF_007989895.1_ASM798989v1_genomic.fna/checkm_result
[2024-01-24 13:47:06,411] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:06,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:06,430] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:06,431] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:06,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989895.1_ASM798989v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:06,431] [INFO] Task started: Blastn
[2024-01-24 13:47:06,431] [INFO] Running command: blastn -query GCF_007989895.1_ASM798989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc29cc66-7101-40a2-9484-491307b0f58a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989895.1_ASM798989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:07,573] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:07,579] [INFO] Selected 9 target genomes.
[2024-01-24 13:47:07,580] [INFO] Target genome list was writen to GCF_007989895.1_ASM798989v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:07,590] [INFO] Task started: fastANI
[2024-01-24 13:47:07,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6cc420e-205d-45bc-9f61-9a26b0ba08ef/GCF_007989895.1_ASM798989v1_genomic.fna.gz --refList GCF_007989895.1_ASM798989v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989895.1_ASM798989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:17,132] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:17,141] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:17,142] [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_012641745.1	s__Pseudoalteromonas peptidolytica	99.9973	1518	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.11	98.10	0.96	0.91	6	conclusive
GCF_005886535.1	s__Pseudoalteromonas sp005886535	83.9207	873	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002208135.1	s__Pseudoalteromonas piscicida_A	83.8096	910	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.45	98.90	0.97	0.95	3	-
GCF_002289345.1	s__Pseudoalteromonas sp002289345	83.5676	900	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.3013	N/A	N/A	N/A	N/A	1	-
GCF_002850255.1	s__Pseudoalteromonas sp002850255	83.4792	908	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.4968	98.33	98.31	0.92	0.91	5	-
GCA_000814665.1	s__Pseudoalteromonas elyakovii	83.4632	921	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0982	98.47	97.40	0.94	0.89	9	-
GCF_016695175.1	s__Pseudoalteromonas sp002591815	83.4539	921	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6666	100.00	100.00	1.00	1.00	2	-
GCF_000238315.3	s__Pseudoalteromonas piscicida	83.3998	919	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0982	97.60	97.35	0.90	0.88	13	-
GCF_002744175.1	s__Pseudoalteromonas piscicida_B	82.815	874	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:17,144] [INFO] GTDB search result was written to GCF_007989895.1_ASM798989v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:17,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:17,148] [INFO] DFAST_QC result json was written to GCF_007989895.1_ASM798989v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:17,148] [INFO] DFAST_QC completed!
[2024-01-24 13:47:17,148] [INFO] Total running time: 0h1m13s