[2024-01-24 13:41:26,232] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:26,235] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:26,235] [INFO] DQC Reference Directory: /var/lib/cwl/stg32789523-5e10-4016-9abd-e99a37f6c41b/dqc_reference
[2024-01-24 13:41:27,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:27,664] [INFO] Task started: Prodigal
[2024-01-24 13:41:27,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg049cdbe9-5371-42ee-a64e-6b28a0b670fd/GCF_008727795.1_ASM872779v1_genomic.fna.gz | prodigal -d GCF_008727795.1_ASM872779v1_genomic.fna/cds.fna -a GCF_008727795.1_ASM872779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:40,661] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:40,661] [INFO] Task started: HMMsearch
[2024-01-24 13:41:40,662] [INFO] Running command: hmmsearch --tblout GCF_008727795.1_ASM872779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32789523-5e10-4016-9abd-e99a37f6c41b/dqc_reference/reference_markers.hmm GCF_008727795.1_ASM872779v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:41,042] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:41,043] [INFO] Found 6/6 markers.
[2024-01-24 13:41:41,089] [INFO] Query marker FASTA was written to GCF_008727795.1_ASM872779v1_genomic.fna/markers.fasta
[2024-01-24 13:41:41,090] [INFO] Task started: Blastn
[2024-01-24 13:41:41,090] [INFO] Running command: blastn -query GCF_008727795.1_ASM872779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32789523-5e10-4016-9abd-e99a37f6c41b/dqc_reference/reference_markers.fasta -out GCF_008727795.1_ASM872779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:41,835] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:41,838] [INFO] Selected 26 target genomes.
[2024-01-24 13:41:41,838] [INFO] Target genome list was writen to GCF_008727795.1_ASM872779v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:41,848] [INFO] Task started: fastANI
[2024-01-24 13:41:41,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg049cdbe9-5371-42ee-a64e-6b28a0b670fd/GCF_008727795.1_ASM872779v1_genomic.fna.gz --refList GCF_008727795.1_ASM872779v1_genomic.fna/target_genomes.txt --output GCF_008727795.1_ASM872779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:58,853] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:58,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32789523-5e10-4016-9abd-e99a37f6c41b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:58,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32789523-5e10-4016-9abd-e99a37f6c41b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:58,872] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:58,872] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:58,872] [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
Nitrincola iocasae	strain=KXZD1103	GCA_008727795.1	2614693	2614693	type	True	100.0	1390	1390	95	conclusive
Nitrincola lacisaponensis	strain=4CA	GCA_000691225.1	267850	267850	type	True	78.8525	487	1390	95	below_threshold
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	78.751	71	1390	95	below_threshold
Nitrincola schmidtii	strain=NCAIM B.02626	GCA_008973715.1	1730894	1730894	type	True	78.4468	246	1390	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	78.1982	102	1390	95	below_threshold
Amphritea japonica	strain=ATCC BAA-1530	GCA_016592435.1	452627	452627	type	True	78.1003	78	1390	95	below_threshold
Nitrincola alkalilacustris	strain=NCAIM B.02612	GCA_008973755.1	1571224	1571224	type	True	77.7694	199	1390	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	77.66	124	1390	95	below_threshold
Nitrincola tapanii	strain=MEB193	GCA_008368715.1	1708751	1708751	type	True	77.6585	181	1390	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	77.4852	107	1390	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	77.473	129	1390	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	77.0714	101	1390	95	below_threshold
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	76.9596	86	1390	95	below_threshold
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	76.373	93	1390	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:58,874] [INFO] DFAST Taxonomy check result was written to GCF_008727795.1_ASM872779v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:58,875] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:58,875] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:58,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32789523-5e10-4016-9abd-e99a37f6c41b/dqc_reference/checkm_data
[2024-01-24 13:41:58,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:58,919] [INFO] Task started: CheckM
[2024-01-24 13:41:58,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008727795.1_ASM872779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008727795.1_ASM872779v1_genomic.fna/checkm_input GCF_008727795.1_ASM872779v1_genomic.fna/checkm_result
[2024-01-24 13:42:38,825] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:38,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:38,849] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:38,849] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:38,850] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008727795.1_ASM872779v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:38,850] [INFO] Task started: Blastn
[2024-01-24 13:42:38,850] [INFO] Running command: blastn -query GCF_008727795.1_ASM872779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32789523-5e10-4016-9abd-e99a37f6c41b/dqc_reference/reference_markers_gtdb.fasta -out GCF_008727795.1_ASM872779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:39,693] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:39,697] [INFO] Selected 15 target genomes.
[2024-01-24 13:42:39,698] [INFO] Target genome list was writen to GCF_008727795.1_ASM872779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:39,746] [INFO] Task started: fastANI
[2024-01-24 13:42:39,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg049cdbe9-5371-42ee-a64e-6b28a0b670fd/GCF_008727795.1_ASM872779v1_genomic.fna.gz --refList GCF_008727795.1_ASM872779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008727795.1_ASM872779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:49,442] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:49,454] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:49,454] [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_008727795.1	s__Nitrincola sp008727795	100.0	1390	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000764495.1	s__Nitrincola sp000764495	84.4923	876	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000691225.1	s__Nitrincola lacisaponensis	78.8426	488	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973715.1	s__Nitrincola schmidtii	78.4468	246	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693685.1	s__Nitrincola sp007693685	78.209	196	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973755.1	s__Nitrincola alkalilacustris	77.7915	199	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008368715.1	s__Nitrincola tapanii	77.6585	181	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339595.1	s__Marinobacterium mangrovicola	77.4852	107	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107855.1	s__Marinobacterium georgiense	77.4461	128	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.23	97.23	0.75	0.75	2	-
GCF_019061305.1	s__Marinobacterium sp019061305	77.2048	111	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084545.1	s__Marinobacterium sp019084545	77.0932	99	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250495.1	s__Marinobacterium sp003250495	77.0464	79	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017051665.1	s__Amphritea spongicola	76.9595	87	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111095.1	s__Amphritea atlantica	76.3929	92	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:49,455] [INFO] GTDB search result was written to GCF_008727795.1_ASM872779v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:49,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:49,461] [INFO] DFAST_QC result json was written to GCF_008727795.1_ASM872779v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:49,461] [INFO] DFAST_QC completed!
[2024-01-24 13:42:49,461] [INFO] Total running time: 0h1m23s