[2024-01-25 18:55:35,493] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:35,495] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:35,495] [INFO] DQC Reference Directory: /var/lib/cwl/stgeaa0a615-160e-4588-b7dd-a6485d855010/dqc_reference
[2024-01-25 18:55:36,610] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:36,611] [INFO] Task started: Prodigal
[2024-01-25 18:55:36,611] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb52a4ad-8d59-4576-ad97-5a872b416239/GCF_024347195.1_ASM2434719v1_genomic.fna.gz | prodigal -d GCF_024347195.1_ASM2434719v1_genomic.fna/cds.fna -a GCF_024347195.1_ASM2434719v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:52,153] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:52,153] [INFO] Task started: HMMsearch
[2024-01-25 18:55:52,153] [INFO] Running command: hmmsearch --tblout GCF_024347195.1_ASM2434719v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeaa0a615-160e-4588-b7dd-a6485d855010/dqc_reference/reference_markers.hmm GCF_024347195.1_ASM2434719v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:52,454] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:52,455] [INFO] Found 6/6 markers.
[2024-01-25 18:55:52,495] [INFO] Query marker FASTA was written to GCF_024347195.1_ASM2434719v1_genomic.fna/markers.fasta
[2024-01-25 18:55:52,495] [INFO] Task started: Blastn
[2024-01-25 18:55:52,495] [INFO] Running command: blastn -query GCF_024347195.1_ASM2434719v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaa0a615-160e-4588-b7dd-a6485d855010/dqc_reference/reference_markers.fasta -out GCF_024347195.1_ASM2434719v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:53,108] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:53,110] [INFO] Selected 21 target genomes.
[2024-01-25 18:55:53,111] [INFO] Target genome list was writen to GCF_024347195.1_ASM2434719v1_genomic.fna/target_genomes.txt
[2024-01-25 18:55:53,126] [INFO] Task started: fastANI
[2024-01-25 18:55:53,126] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb52a4ad-8d59-4576-ad97-5a872b416239/GCF_024347195.1_ASM2434719v1_genomic.fna.gz --refList GCF_024347195.1_ASM2434719v1_genomic.fna/target_genomes.txt --output GCF_024347195.1_ASM2434719v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:10,670] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:10,670] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeaa0a615-160e-4588-b7dd-a6485d855010/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:10,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeaa0a615-160e-4588-b7dd-a6485d855010/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:10,680] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:56:10,680] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:56:10,680] [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
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	89.1485	1422	1736	95	below_threshold
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	82.2655	1071	1736	95	below_threshold
Amphritea japonica	strain=ATCC BAA-1530	GCA_016592435.1	452627	452627	type	True	79.3639	192	1736	95	below_threshold
Amphritea japonica	strain=JCM 14782	GCA_024347275.1	452627	452627	type	True	79.2587	187	1736	95	below_threshold
Amphritea balenae	strain=JAMM 1525	GCA_003858655.1	452629	452629	type	True	78.6159	257	1736	95	below_threshold
Amphritea balenae	strain=JCM 14781	GCA_014646975.1	452629	452629	type	True	78.5287	250	1736	95	below_threshold
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	78.3604	236	1736	95	below_threshold
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	78.2263	236	1736	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	77.8552	52	1736	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	77.1876	59	1736	95	below_threshold
Nitrincola lacisaponensis	strain=4CA	GCA_000691225.1	267850	267850	type	True	76.9873	96	1736	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	76.9292	146	1736	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	76.7321	147	1736	95	below_threshold
Marinobacter aromaticivorans	strain=D15-8P	GCA_002806975.1	1494078	1494078	type	True	75.9404	56	1736	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:10,681] [INFO] DFAST Taxonomy check result was written to GCF_024347195.1_ASM2434719v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:10,682] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:10,682] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:10,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeaa0a615-160e-4588-b7dd-a6485d855010/dqc_reference/checkm_data
[2024-01-25 18:56:10,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:10,734] [INFO] Task started: CheckM
[2024-01-25 18:56:10,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347195.1_ASM2434719v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347195.1_ASM2434719v1_genomic.fna/checkm_input GCF_024347195.1_ASM2434719v1_genomic.fna/checkm_result
[2024-01-25 18:57:01,068] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:01,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:01,092] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:01,092] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:01,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347195.1_ASM2434719v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:01,093] [INFO] Task started: Blastn
[2024-01-25 18:57:01,093] [INFO] Running command: blastn -query GCF_024347195.1_ASM2434719v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaa0a615-160e-4588-b7dd-a6485d855010/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347195.1_ASM2434719v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:02,067] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:02,070] [INFO] Selected 18 target genomes.
[2024-01-25 18:57:02,070] [INFO] Target genome list was writen to GCF_024347195.1_ASM2434719v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:02,092] [INFO] Task started: fastANI
[2024-01-25 18:57:02,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb52a4ad-8d59-4576-ad97-5a872b416239/GCF_024347195.1_ASM2434719v1_genomic.fna.gz --refList GCF_024347195.1_ASM2434719v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347195.1_ASM2434719v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:17,392] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:17,401] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:57:17,402] [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_017051665.1	s__Amphritea spongicola	89.1551	1421	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016592435.1	s__Amphritea japonica	79.4592	193	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003858655.1	s__Amphritea balenae	78.6159	257	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	100.00	100.00	0.99	0.99	2	-
GCF_018860855.1	s__Amphritea atlantica_A	78.4837	167	1736	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	78.3546	235	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924235.1	s__Amphritea sp016924235	78.3477	232	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.30	99.30	0.95	0.95	2	-
GCA_018067325.1	s__Amphritea sp018067325	78.2414	135	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.51	99.51	0.92	0.92	2	-
GCA_000330845.1	s__Pseudocitrobacter sp000330845	78.1282	50	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudocitrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223185.1	s__Amphritea sp018223185	78.0358	245	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000691225.1	s__Nitrincola lacisaponensis	77.0081	95	1736	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	76.9115	147	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528745.1	s__Marinobacterium_A profundum	76.7324	146	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806975.1	s__Marinobacter aromaticivorans	75.9404	56	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:17,403] [INFO] GTDB search result was written to GCF_024347195.1_ASM2434719v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:17,404] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:17,407] [INFO] DFAST_QC result json was written to GCF_024347195.1_ASM2434719v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:17,407] [INFO] DFAST_QC completed!
[2024-01-25 18:57:17,407] [INFO] Total running time: 0h1m42s