[2024-01-25 20:23:05,667] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:05,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:05,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e25c244-73a6-4fd2-8f43-1f0867b90799/dqc_reference
[2024-01-25 20:23:06,792] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:06,793] [INFO] Task started: Prodigal
[2024-01-25 20:23:06,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg362950b6-067d-4470-979a-c35b3c7ca05a/GCF_030295915.1_ASM3029591v1_genomic.fna.gz | prodigal -d GCF_030295915.1_ASM3029591v1_genomic.fna/cds.fna -a GCF_030295915.1_ASM3029591v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:13,865] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:13,865] [INFO] Task started: HMMsearch
[2024-01-25 20:23:13,865] [INFO] Running command: hmmsearch --tblout GCF_030295915.1_ASM3029591v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e25c244-73a6-4fd2-8f43-1f0867b90799/dqc_reference/reference_markers.hmm GCF_030295915.1_ASM3029591v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:14,115] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:14,116] [INFO] Found 6/6 markers.
[2024-01-25 20:23:14,147] [INFO] Query marker FASTA was written to GCF_030295915.1_ASM3029591v1_genomic.fna/markers.fasta
[2024-01-25 20:23:14,147] [INFO] Task started: Blastn
[2024-01-25 20:23:14,147] [INFO] Running command: blastn -query GCF_030295915.1_ASM3029591v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e25c244-73a6-4fd2-8f43-1f0867b90799/dqc_reference/reference_markers.fasta -out GCF_030295915.1_ASM3029591v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:14,819] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:14,822] [INFO] Selected 23 target genomes.
[2024-01-25 20:23:14,822] [INFO] Target genome list was writen to GCF_030295915.1_ASM3029591v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:14,869] [INFO] Task started: fastANI
[2024-01-25 20:23:14,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg362950b6-067d-4470-979a-c35b3c7ca05a/GCF_030295915.1_ASM3029591v1_genomic.fna.gz --refList GCF_030295915.1_ASM3029591v1_genomic.fna/target_genomes.txt --output GCF_030295915.1_ASM3029591v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:32,334] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:32,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e25c244-73a6-4fd2-8f43-1f0867b90799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:32,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e25c244-73a6-4fd2-8f43-1f0867b90799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:32,344] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:23:32,344] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:23:32,345] [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
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.7123	205	1298	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	78.6898	322	1298	95	below_threshold
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	78.3819	187	1298	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	78.1243	67	1298	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	78.012	215	1298	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001652445.1	1763536	1763536	type	True	78.0073	105	1298	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.9015	138	1298	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.853	221	1298	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.7651	156	1298	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.7506	195	1298	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.512	188	1298	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.4984	188	1298	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.3816	166	1298	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	76.8352	60	1298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:32,346] [INFO] DFAST Taxonomy check result was written to GCF_030295915.1_ASM3029591v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:32,346] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:32,346] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:32,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e25c244-73a6-4fd2-8f43-1f0867b90799/dqc_reference/checkm_data
[2024-01-25 20:23:32,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:32,386] [INFO] Task started: CheckM
[2024-01-25 20:23:32,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030295915.1_ASM3029591v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030295915.1_ASM3029591v1_genomic.fna/checkm_input GCF_030295915.1_ASM3029591v1_genomic.fna/checkm_result
[2024-01-25 20:23:57,381] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:57,382] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:57,399] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:57,399] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:57,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030295915.1_ASM3029591v1_genomic.fna/markers.fasta)
[2024-01-25 20:23:57,399] [INFO] Task started: Blastn
[2024-01-25 20:23:57,399] [INFO] Running command: blastn -query GCF_030295915.1_ASM3029591v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e25c244-73a6-4fd2-8f43-1f0867b90799/dqc_reference/reference_markers_gtdb.fasta -out GCF_030295915.1_ASM3029591v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:58,451] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:58,453] [INFO] Selected 20 target genomes.
[2024-01-25 20:23:58,454] [INFO] Target genome list was writen to GCF_030295915.1_ASM3029591v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:58,480] [INFO] Task started: fastANI
[2024-01-25 20:23:58,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg362950b6-067d-4470-979a-c35b3c7ca05a/GCF_030295915.1_ASM3029591v1_genomic.fna.gz --refList GCF_030295915.1_ASM3029591v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030295915.1_ASM3029591v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:11,849] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:11,860] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:24:11,860] [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_001913705.1	s__Thalassotalea_C sp001913705	80.7872	622	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656435.1	s__Thalassotalea_C marina	78.6787	323	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295665.1	s__Litorilituus sediminis	78.5994	200	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832865.1	s__Colwellia sp009832865	78.5592	181	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	78.3869	191	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017168195.1	s__G2M2-11 sp017168195	78.3567	256	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__G2M2-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001767295.1	s__Colwellia_A sp001767295	78.1719	182	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	96.63	96.27	0.86	0.85	17	-
GCF_014207645.1	s__Thalassotalea_B piscium	78.0446	213	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	78.0252	204	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	77.9751	174	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	77.9609	195	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	77.8622	181	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545765.1	s__Litorilituus sp003545765	77.8046	192	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843355.2	s__Colwellia echini	77.7914	154	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491935.1	s__GCA-2401725 sp015491935	77.3324	150	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003545415.1	s__Colwellia sp003545415	77.2185	120	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	77.1434	167	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765685.1	s__Colwellia sp016765685	77.0282	86	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:11,861] [INFO] GTDB search result was written to GCF_030295915.1_ASM3029591v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:11,862] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:11,865] [INFO] DFAST_QC result json was written to GCF_030295915.1_ASM3029591v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:11,865] [INFO] DFAST_QC completed!
[2024-01-25 20:24:11,865] [INFO] Total running time: 0h1m6s