[2024-01-24 11:34:36,882] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:36,884] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:36,885] [INFO] DQC Reference Directory: /var/lib/cwl/stg98bbbc98-0278-40ec-b87f-0d8dba8db57e/dqc_reference
[2024-01-24 11:34:39,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:39,642] [INFO] Task started: Prodigal
[2024-01-24 11:34:39,642] [INFO] Running command: gunzip -c /var/lib/cwl/stg77a290c9-0e7a-4247-af61-196c12d9feb3/GCF_030161415.1_ASM3016141v1_genomic.fna.gz | prodigal -d GCF_030161415.1_ASM3016141v1_genomic.fna/cds.fna -a GCF_030161415.1_ASM3016141v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:46,912] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:46,913] [INFO] Task started: HMMsearch
[2024-01-24 11:34:46,913] [INFO] Running command: hmmsearch --tblout GCF_030161415.1_ASM3016141v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98bbbc98-0278-40ec-b87f-0d8dba8db57e/dqc_reference/reference_markers.hmm GCF_030161415.1_ASM3016141v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:47,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:47,266] [INFO] Found 6/6 markers.
[2024-01-24 11:34:47,295] [INFO] Query marker FASTA was written to GCF_030161415.1_ASM3016141v1_genomic.fna/markers.fasta
[2024-01-24 11:34:47,295] [INFO] Task started: Blastn
[2024-01-24 11:34:47,295] [INFO] Running command: blastn -query GCF_030161415.1_ASM3016141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98bbbc98-0278-40ec-b87f-0d8dba8db57e/dqc_reference/reference_markers.fasta -out GCF_030161415.1_ASM3016141v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:48,090] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:48,094] [INFO] Selected 21 target genomes.
[2024-01-24 11:34:48,095] [INFO] Target genome list was writen to GCF_030161415.1_ASM3016141v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:48,123] [INFO] Task started: fastANI
[2024-01-24 11:34:48,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg77a290c9-0e7a-4247-af61-196c12d9feb3/GCF_030161415.1_ASM3016141v1_genomic.fna.gz --refList GCF_030161415.1_ASM3016141v1_genomic.fna/target_genomes.txt --output GCF_030161415.1_ASM3016141v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:02,616] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:02,617] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98bbbc98-0278-40ec-b87f-0d8dba8db57e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:02,617] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98bbbc98-0278-40ec-b87f-0d8dba8db57e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:02,632] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:02,632] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:02,633] [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
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	79.3049	229	1169	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	78.6913	153	1169	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.3736	189	1169	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	78.3518	157	1169	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.1721	147	1169	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	78.1544	178	1169	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001831495.1	1763536	1763536	type	True	78.1539	150	1169	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	78.1111	158	1169	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.0688	163	1169	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001652445.1	1763536	1763536	type	True	78.0399	146	1169	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.8797	154	1169	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.8204	196	1169	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.4637	176	1169	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	77.3852	53	1169	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	77.3598	144	1169	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	76.602	52	1169	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	76.5778	65	1169	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	76.4198	61	1169	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	76.1427	64	1169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:02,634] [INFO] DFAST Taxonomy check result was written to GCF_030161415.1_ASM3016141v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:02,635] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:02,635] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:02,635] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98bbbc98-0278-40ec-b87f-0d8dba8db57e/dqc_reference/checkm_data
[2024-01-24 11:35:02,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:02,672] [INFO] Task started: CheckM
[2024-01-24 11:35:02,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161415.1_ASM3016141v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161415.1_ASM3016141v1_genomic.fna/checkm_input GCF_030161415.1_ASM3016141v1_genomic.fna/checkm_result
[2024-01-24 11:35:29,454] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:29,455] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:29,474] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:29,474] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:29,474] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161415.1_ASM3016141v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:29,475] [INFO] Task started: Blastn
[2024-01-24 11:35:29,475] [INFO] Running command: blastn -query GCF_030161415.1_ASM3016141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98bbbc98-0278-40ec-b87f-0d8dba8db57e/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161415.1_ASM3016141v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:30,623] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:30,626] [INFO] Selected 26 target genomes.
[2024-01-24 11:35:30,626] [INFO] Target genome list was writen to GCF_030161415.1_ASM3016141v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:30,664] [INFO] Task started: fastANI
[2024-01-24 11:35:30,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg77a290c9-0e7a-4247-af61-196c12d9feb3/GCF_030161415.1_ASM3016141v1_genomic.fna.gz --refList GCF_030161415.1_ASM3016141v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161415.1_ASM3016141v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:47,505] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:47,524] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:35:47,525] [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_014898095.1	s__Thalassotalea sp014898095	79.9258	513	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932965.1	s__Thalassotalea algicola	79.3311	229	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390395.1	s__Thalassotalea euphylliae_C	79.2243	212	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390335.1	s__Thalassotalea euphylliae_B	78.8316	168	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207645.1	s__Thalassotalea_B piscium	78.6913	153	1169	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_017744155.1	s__Thalassotalea sp017744155	78.5076	172	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295665.1	s__Litorilituus sediminis	78.3547	190	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860755.1	s__Colwellia sp018860755	78.3517	174	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017168195.1	s__G2M2-11 sp017168195	78.3284	159	1169	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_007097525.1	s__Thalassotalea_A sp007097525	78.1839	168	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111755.1	s__Thalassotalea_D agarivorans	78.1111	158	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913705.1	s__Thalassotalea_C sp001913705	78.0061	159	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	77.9489	183	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	77.9271	183	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	77.8996	181	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104475.1	s__Cognaticolwellia mytili	77.8359	195	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	77.7459	161	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002076895.1	s__Cognaticolwellia beringensis	77.7128	191	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832865.1	s__Colwellia sp009832865	77.5583	174	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215295.1	s__Colwellia_A sp013215295	77.5203	175	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954275.1	s__Colwellia demingiae	77.4616	174	1169	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	77.3256	148	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765535.1	s__GCA-2401725 sp016765535	77.2247	124	1169	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_015491935.1	s__GCA-2401725 sp015491935	77.2179	149	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440345.1	s__Colwellia sp001440345	77.183	148	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401725.1	s__GCA-2401725 sp002401725	77.0034	126	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:47,526] [INFO] GTDB search result was written to GCF_030161415.1_ASM3016141v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:47,527] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:47,532] [INFO] DFAST_QC result json was written to GCF_030161415.1_ASM3016141v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:47,532] [INFO] DFAST_QC completed!
[2024-01-24 11:35:47,532] [INFO] Total running time: 0h1m11s