[2024-01-24 12:22:06,581] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:06,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:06,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg2644db86-e1cb-458a-906c-b706d3105380/dqc_reference
[2024-01-24 12:22:07,781] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:07,782] [INFO] Task started: Prodigal
[2024-01-24 12:22:07,782] [INFO] Running command: gunzip -c /var/lib/cwl/stg0990bd3f-5ed7-4bf6-8543-b18539f8c4d5/GCF_000238355.1_Phal_1.0_genomic.fna.gz | prodigal -d GCF_000238355.1_Phal_1.0_genomic.fna/cds.fna -a GCF_000238355.1_Phal_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:18,629] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:18,629] [INFO] Task started: HMMsearch
[2024-01-24 12:22:18,630] [INFO] Running command: hmmsearch --tblout GCF_000238355.1_Phal_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2644db86-e1cb-458a-906c-b706d3105380/dqc_reference/reference_markers.hmm GCF_000238355.1_Phal_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:18,975] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:18,976] [INFO] Found 6/6 markers.
[2024-01-24 12:22:19,016] [INFO] Query marker FASTA was written to GCF_000238355.1_Phal_1.0_genomic.fna/markers.fasta
[2024-01-24 12:22:19,017] [INFO] Task started: Blastn
[2024-01-24 12:22:19,017] [INFO] Running command: blastn -query GCF_000238355.1_Phal_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg2644db86-e1cb-458a-906c-b706d3105380/dqc_reference/reference_markers.fasta -out GCF_000238355.1_Phal_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:19,817] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:19,819] [INFO] Selected 12 target genomes.
[2024-01-24 12:22:19,820] [INFO] Target genome list was writen to GCF_000238355.1_Phal_1.0_genomic.fna/target_genomes.txt
[2024-01-24 12:22:19,825] [INFO] Task started: fastANI
[2024-01-24 12:22:19,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg0990bd3f-5ed7-4bf6-8543-b18539f8c4d5/GCF_000238355.1_Phal_1.0_genomic.fna.gz --refList GCF_000238355.1_Phal_1.0_genomic.fna/target_genomes.txt --output GCF_000238355.1_Phal_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:31,272] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:31,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2644db86-e1cb-458a-906c-b706d3105380/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:31,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2644db86-e1cb-458a-906c-b706d3105380/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:31,284] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:31,284] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:31,284] [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 prydzensis	strain=ACAM 620	GCA_014925355.1	182141	182141	type	True	86.7233	1274	1648	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	86.6997	1264	1648	95	below_threshold
Pseudoalteromonas ostreae	strain=hOe-66	GCA_018069805.1	2774154	2774154	type	True	83.878	995	1648	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	83.7797	1088	1648	95	below_threshold
Pseudoalteromonas neustonica	strain=PAMC 28425	GCA_001653135.1	1840331	1840331	type	True	82.2834	893	1648	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	80.4811	604	1648	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	80.395	586	1648	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	80.2296	592	1648	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	78.6921	238	1648	95	below_threshold
Vibrio ulleungensis	strain=188UL20-2	GCA_016900875.1	2807619	2807619	type	True	76.4	53	1648	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	76.2664	63	1648	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	75.8937	52	1648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:31,286] [INFO] DFAST Taxonomy check result was written to GCF_000238355.1_Phal_1.0_genomic.fna/tc_result.tsv
[2024-01-24 12:22:31,286] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:31,286] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:31,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2644db86-e1cb-458a-906c-b706d3105380/dqc_reference/checkm_data
[2024-01-24 12:22:31,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:31,334] [INFO] Task started: CheckM
[2024-01-24 12:22:31,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000238355.1_Phal_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000238355.1_Phal_1.0_genomic.fna/checkm_input GCF_000238355.1_Phal_1.0_genomic.fna/checkm_result
[2024-01-24 12:23:08,201] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:08,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:08,231] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:08,231] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:08,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000238355.1_Phal_1.0_genomic.fna/markers.fasta)
[2024-01-24 12:23:08,232] [INFO] Task started: Blastn
[2024-01-24 12:23:08,232] [INFO] Running command: blastn -query GCF_000238355.1_Phal_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg2644db86-e1cb-458a-906c-b706d3105380/dqc_reference/reference_markers_gtdb.fasta -out GCF_000238355.1_Phal_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:09,363] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:09,372] [INFO] Selected 9 target genomes.
[2024-01-24 12:23:09,372] [INFO] Target genome list was writen to GCF_000238355.1_Phal_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:09,386] [INFO] Task started: fastANI
[2024-01-24 12:23:09,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg0990bd3f-5ed7-4bf6-8543-b18539f8c4d5/GCF_000238355.1_Phal_1.0_genomic.fna.gz --refList GCF_000238355.1_Phal_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000238355.1_Phal_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:20,389] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:20,403] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:20,403] [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_000238355.1	s__Pseudoalteromonas haloplanktis	100.0	1644	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.55	99.12	0.96	0.93	3	conclusive
GCF_001661495.1	s__Pseudoalteromonas prydzensis	86.7006	1264	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.53	97.08	0.91	0.82	3	-
GCA_011050055.1	s__Pseudoalteromonas prydzensis_A	85.7229	1109	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927645.1	s__Pseudoalteromonas arctica_A	84.0102	921	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069805.1	s__Pseudoalteromonas sp018069805	83.8805	994	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498845.1	s__Pseudoalteromonas rhizosphaerae	83.7797	1088	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.81	97.24	0.86	0.81	17	-
GCF_001653135.1	s__Pseudoalteromonas neustonica	82.2555	898	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.11	98.62	0.93	0.89	5	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	80.4516	606	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
GCF_000238275.3	s__Pseudoalteromonas undina	80.2354	591	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:20,405] [INFO] GTDB search result was written to GCF_000238355.1_Phal_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:20,406] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:20,409] [INFO] DFAST_QC result json was written to GCF_000238355.1_Phal_1.0_genomic.fna/dqc_result.json
[2024-01-24 12:23:20,409] [INFO] DFAST_QC completed!
[2024-01-24 12:23:20,409] [INFO] Total running time: 0h1m14s