[2024-01-24 13:57:45,445] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:45,447] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:45,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg347aebe3-bf47-4e74-93c7-2e1f293abd3f/dqc_reference
[2024-01-24 13:57:46,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:46,837] [INFO] Task started: Prodigal
[2024-01-24 13:57:46,837] [INFO] Running command: gunzip -c /var/lib/cwl/stg2906cbf2-f745-414c-86c4-60afe9c64e23/GCF_004103265.1_ASM410326v1_genomic.fna.gz | prodigal -d GCF_004103265.1_ASM410326v1_genomic.fna/cds.fna -a GCF_004103265.1_ASM410326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:56,921] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:56,922] [INFO] Task started: HMMsearch
[2024-01-24 13:57:56,922] [INFO] Running command: hmmsearch --tblout GCF_004103265.1_ASM410326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg347aebe3-bf47-4e74-93c7-2e1f293abd3f/dqc_reference/reference_markers.hmm GCF_004103265.1_ASM410326v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:57,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:57,266] [INFO] Found 6/6 markers.
[2024-01-24 13:57:57,311] [INFO] Query marker FASTA was written to GCF_004103265.1_ASM410326v1_genomic.fna/markers.fasta
[2024-01-24 13:57:57,312] [INFO] Task started: Blastn
[2024-01-24 13:57:57,312] [INFO] Running command: blastn -query GCF_004103265.1_ASM410326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg347aebe3-bf47-4e74-93c7-2e1f293abd3f/dqc_reference/reference_markers.fasta -out GCF_004103265.1_ASM410326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:58,074] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:58,078] [INFO] Selected 16 target genomes.
[2024-01-24 13:57:58,078] [INFO] Target genome list was writen to GCF_004103265.1_ASM410326v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:58,093] [INFO] Task started: fastANI
[2024-01-24 13:57:58,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg2906cbf2-f745-414c-86c4-60afe9c64e23/GCF_004103265.1_ASM410326v1_genomic.fna.gz --refList GCF_004103265.1_ASM410326v1_genomic.fna/target_genomes.txt --output GCF_004103265.1_ASM410326v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:13,556] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:13,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg347aebe3-bf47-4e74-93c7-2e1f293abd3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:13,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg347aebe3-bf47-4e74-93c7-2e1f293abd3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:13,570] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:58:13,571] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:13,571] [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 phenolica	strain=O-BC30	GCA_004103265.1	161398	161398	suspected-type	True	100.0	1456	1469	95	conclusive
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	99.9568	1468	1469	95	conclusive
Pseudoalteromonas phenolica	strain=KCTC 12086	GCA_001444405.1	161398	161398	suspected-type	True	99.9565	1469	1469	95	conclusive
Pseudoalteromonas amylolytica	strain=JW1	GCA_001854605.1	1859457	1859457	type	True	79.1735	292	1469	95	below_threshold
Pseudoalteromonas byunsanensis	strain=JCM 12483	GCA_001854475.1	327939	327939	type	True	79.1554	281	1469	95	below_threshold
Pseudoalteromonas luteoviolacea	strain=DSM 6061	GCA_001625655.1	43657	43657	suspected-type	True	79.0242	259	1469	95	below_threshold
Pseudoalteromonas piscicida	strain=ATCC 15057	GCA_000382005.1	43662	43662	type	True	78.8959	287	1469	95	below_threshold
Pseudoalteromonas citrea	strain=DSM 8771	GCA_000238375.4	43655	43655	type	True	78.8561	300	1469	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	78.8007	282	1469	95	below_threshold
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	78.5134	274	1469	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	78.3284	232	1469	95	below_threshold
Pseudoalteromonas neustonica	strain=PAMC 28425	GCA_001653135.1	1840331	1840331	type	True	78.1242	233	1469	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	76.7371	55	1469	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	76.545	63	1469	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	76.1168	56	1469	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	75.9083	51	1469	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:13,573] [INFO] DFAST Taxonomy check result was written to GCF_004103265.1_ASM410326v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:13,574] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:13,574] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:13,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg347aebe3-bf47-4e74-93c7-2e1f293abd3f/dqc_reference/checkm_data
[2024-01-24 13:58:13,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:13,622] [INFO] Task started: CheckM
[2024-01-24 13:58:13,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004103265.1_ASM410326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004103265.1_ASM410326v1_genomic.fna/checkm_input GCF_004103265.1_ASM410326v1_genomic.fna/checkm_result
[2024-01-24 13:58:48,050] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:48,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:48,071] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:48,072] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:48,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004103265.1_ASM410326v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:48,073] [INFO] Task started: Blastn
[2024-01-24 13:58:48,073] [INFO] Running command: blastn -query GCF_004103265.1_ASM410326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg347aebe3-bf47-4e74-93c7-2e1f293abd3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004103265.1_ASM410326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:48,991] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:48,994] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:48,994] [INFO] Target genome list was writen to GCF_004103265.1_ASM410326v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:49,004] [INFO] Task started: fastANI
[2024-01-24 13:58:49,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg2906cbf2-f745-414c-86c4-60afe9c64e23/GCF_004103265.1_ASM410326v1_genomic.fna.gz --refList GCF_004103265.1_ASM410326v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004103265.1_ASM410326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:02,529] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:02,545] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:02,545] [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_001444405.1	s__Pseudoalteromonas phenolica	99.9565	1469	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.52	98.61	0.97	0.92	4	conclusive
GCF_005876835.1	s__Pseudoalteromonas phenolica_B	90.8982	1218	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005886345.1	s__Pseudoalteromonas phenolica_A	88.8419	1054	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.97	0.91	0.89	3	-
GCF_000814765.1	s__Pseudoalteromonas luteoviolacea_H	79.2644	285	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	95.23	95.23	0.92	0.92	2	-
GCF_001750165.1	s__Pseudoalteromonas luteoviolacea_G	79.2586	307	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	99.99	1.00	1.00	5	-
GCF_001854605.1	s__Pseudoalteromonas amylolytica	79.1656	292	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001854475.1	s__Pseudoalteromonas byunsanensis	79.1554	281	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014694405.1	s__Pseudoalteromonas sp014694405	79.0701	317	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176705.1	s__Pseudoalteromonas sp009176705	78.9708	313	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238375.3	s__Pseudoalteromonas citrea	78.8786	298	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004103285.1	s__Pseudoalteromonas sp004103285	78.8695	271	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.27	99.27	0.97	0.97	2	-
GCF_013391845.1	s__Pseudoalteromonas sp002685175	78.5557	247	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.05	98.96	0.91	0.83	5	-
GCF_000238355.1	s__Pseudoalteromonas haloplanktis	78.0192	234	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.55	99.12	0.96	0.93	3	-
GCF_000498095.1	s__Pseudoalteromonas sp000498095	77.8509	197	1469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.86	97.76	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:02,547] [INFO] GTDB search result was written to GCF_004103265.1_ASM410326v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:02,547] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:02,551] [INFO] DFAST_QC result json was written to GCF_004103265.1_ASM410326v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:02,552] [INFO] DFAST_QC completed!
[2024-01-24 13:59:02,552] [INFO] Total running time: 0h1m17s