[2024-01-24 12:40:06,740] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:06,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:06,742] [INFO] DQC Reference Directory: /var/lib/cwl/stgebc0e970-a5b7-40bb-9399-4ea8a81d6bd1/dqc_reference
[2024-01-24 12:40:08,079] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,080] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,081] [INFO] Running command: gunzip -c /var/lib/cwl/stg48d59ede-0892-42dc-b23b-672a3903b869/GCF_032461525.1_ASM3246152v1_genomic.fna.gz | prodigal -d GCF_032461525.1_ASM3246152v1_genomic.fna/cds.fna -a GCF_032461525.1_ASM3246152v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:15,876] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:15,877] [INFO] Task started: HMMsearch
[2024-01-24 12:40:15,877] [INFO] Running command: hmmsearch --tblout GCF_032461525.1_ASM3246152v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebc0e970-a5b7-40bb-9399-4ea8a81d6bd1/dqc_reference/reference_markers.hmm GCF_032461525.1_ASM3246152v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:16,114] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:16,115] [INFO] Found 6/6 markers.
[2024-01-24 12:40:16,149] [INFO] Query marker FASTA was written to GCF_032461525.1_ASM3246152v1_genomic.fna/markers.fasta
[2024-01-24 12:40:16,149] [INFO] Task started: Blastn
[2024-01-24 12:40:16,149] [INFO] Running command: blastn -query GCF_032461525.1_ASM3246152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebc0e970-a5b7-40bb-9399-4ea8a81d6bd1/dqc_reference/reference_markers.fasta -out GCF_032461525.1_ASM3246152v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:16,877] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:16,880] [INFO] Selected 23 target genomes.
[2024-01-24 12:40:16,880] [INFO] Target genome list was writen to GCF_032461525.1_ASM3246152v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:16,888] [INFO] Task started: fastANI
[2024-01-24 12:40:16,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg48d59ede-0892-42dc-b23b-672a3903b869/GCF_032461525.1_ASM3246152v1_genomic.fna.gz --refList GCF_032461525.1_ASM3246152v1_genomic.fna/target_genomes.txt --output GCF_032461525.1_ASM3246152v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:31,052] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:31,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebc0e970-a5b7-40bb-9399-4ea8a81d6bd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:31,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebc0e970-a5b7-40bb-9399-4ea8a81d6bd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:31,066] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:31,066] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:31,067] [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
Psychrosphaera saromensis	strain=SA4-48	GCA_002954545.1	716813	716813	type	True	81.4773	669	1285	95	below_threshold
Psychrosphaera saromensis	strain=KCTC 23240	GCA_014652155.1	716813	716813	type	True	81.2853	655	1285	95	below_threshold
Psychrosphaera aestuarii	strain=PSC101	GCA_017948405.1	1266052	1266052	type	True	79.004	185	1285	95	below_threshold
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	78.6489	164	1285	95	below_threshold
Pseudoalteromonas piratica	strain=OCN003	GCA_000788395.1	1348114	1348114	type	True	77.6966	81	1285	95	below_threshold
Shewanella japonica	strain=KCTC 22435	GCA_002075795.1	93973	93973	type	True	77.2636	79	1285	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	76.7372	81	1285	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	76.6365	101	1285	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	76.5105	91	1285	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	76.3185	63	1285	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_014647215.1	1028752	1028752	type	True	76.1795	61	1285	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	76.1774	62	1285	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	76.1637	58	1285	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	76.1614	69	1285	95	below_threshold
Vibrio sinensis	strain=BEI233	GCA_003605645.1	2302434	2302434	type	True	76.0066	50	1285	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	75.8272	72	1285	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:31,068] [INFO] DFAST Taxonomy check result was written to GCF_032461525.1_ASM3246152v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:31,069] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:31,069] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:31,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebc0e970-a5b7-40bb-9399-4ea8a81d6bd1/dqc_reference/checkm_data
[2024-01-24 12:40:31,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:31,109] [INFO] Task started: CheckM
[2024-01-24 12:40:31,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_032461525.1_ASM3246152v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_032461525.1_ASM3246152v1_genomic.fna/checkm_input GCF_032461525.1_ASM3246152v1_genomic.fna/checkm_result
[2024-01-24 12:40:58,094] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:58,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:58,119] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:58,119] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:58,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_032461525.1_ASM3246152v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:58,120] [INFO] Task started: Blastn
[2024-01-24 12:40:58,120] [INFO] Running command: blastn -query GCF_032461525.1_ASM3246152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebc0e970-a5b7-40bb-9399-4ea8a81d6bd1/dqc_reference/reference_markers_gtdb.fasta -out GCF_032461525.1_ASM3246152v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:59,199] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:59,202] [INFO] Selected 12 target genomes.
[2024-01-24 12:40:59,202] [INFO] Target genome list was writen to GCF_032461525.1_ASM3246152v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:59,212] [INFO] Task started: fastANI
[2024-01-24 12:40:59,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg48d59ede-0892-42dc-b23b-672a3903b869/GCF_032461525.1_ASM3246152v1_genomic.fna.gz --refList GCF_032461525.1_ASM3246152v1_genomic.fna/target_genomes_gtdb.txt --output GCF_032461525.1_ASM3246152v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:07,490] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:07,497] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:07,498] [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_018860345.1	s__Psychrosphaera sp018860345	97.6089	1129	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002954545.1	s__Psychrosphaera saromensis	81.5006	669	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009728465.1	s__Psychrosphaera haliotis	79.2323	191	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948405.1	s__Psychrosphaera aestuarii	79.0241	187	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017638545.1	s__Psychrosphaera sp017638545	78.6489	164	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861025.1	s__Psychrosphaera sp018861025	78.4457	206	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001767295.1	s__Colwellia_A sp001767295	77.763	105	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	96.63	96.27	0.86	0.85	17	-
GCA_013373245.1	s__Psychrosphaera sp013373245	77.3203	186	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014076845.1	s__Colwellia_A sp014076845	77.1298	76	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	99.15	95.49	0.95	0.86	8	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:07,499] [INFO] GTDB search result was written to GCF_032461525.1_ASM3246152v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:07,500] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:07,511] [INFO] DFAST_QC result json was written to GCF_032461525.1_ASM3246152v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:07,511] [INFO] DFAST_QC completed!
[2024-01-24 12:41:07,511] [INFO] Total running time: 0h1m1s