[2024-01-24 13:24:12,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:12,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:12,791] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd0ff1cf-821d-4019-8f66-aaaa3624e106/dqc_reference
[2024-01-24 13:24:14,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:14,017] [INFO] Task started: Prodigal
[2024-01-24 13:24:14,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg295e7413-daa7-487d-be02-052db4e693b4/GCF_012932965.1_ASM1293296v1_genomic.fna.gz | prodigal -d GCF_012932965.1_ASM1293296v1_genomic.fna/cds.fna -a GCF_012932965.1_ASM1293296v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:21,978] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:21,978] [INFO] Task started: HMMsearch
[2024-01-24 13:24:21,978] [INFO] Running command: hmmsearch --tblout GCF_012932965.1_ASM1293296v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd0ff1cf-821d-4019-8f66-aaaa3624e106/dqc_reference/reference_markers.hmm GCF_012932965.1_ASM1293296v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:22,209] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:22,210] [INFO] Found 6/6 markers.
[2024-01-24 13:24:22,245] [INFO] Query marker FASTA was written to GCF_012932965.1_ASM1293296v1_genomic.fna/markers.fasta
[2024-01-24 13:24:22,246] [INFO] Task started: Blastn
[2024-01-24 13:24:22,246] [INFO] Running command: blastn -query GCF_012932965.1_ASM1293296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd0ff1cf-821d-4019-8f66-aaaa3624e106/dqc_reference/reference_markers.fasta -out GCF_012932965.1_ASM1293296v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:22,933] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:22,936] [INFO] Selected 20 target genomes.
[2024-01-24 13:24:22,937] [INFO] Target genome list was writen to GCF_012932965.1_ASM1293296v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:22,960] [INFO] Task started: fastANI
[2024-01-24 13:24:22,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg295e7413-daa7-487d-be02-052db4e693b4/GCF_012932965.1_ASM1293296v1_genomic.fna.gz --refList GCF_012932965.1_ASM1293296v1_genomic.fna/target_genomes.txt --output GCF_012932965.1_ASM1293296v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:36,307] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:36,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd0ff1cf-821d-4019-8f66-aaaa3624e106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:36,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd0ff1cf-821d-4019-8f66-aaaa3624e106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:36,319] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:24:36,319] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:24:36,319] [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	100.0	1346	1349	95	conclusive
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	78.6409	173	1349	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.3544	207	1349	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	78.3519	136	1349	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	78.292	190	1349	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	78.2305	188	1349	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.675	163	1349	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.5704	182	1349	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.5695	159	1349	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.4255	156	1349	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.4	160	1349	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	77.047	149	1349	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	76.9649	53	1349	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	76.3035	60	1349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:24:36,321] [INFO] DFAST Taxonomy check result was written to GCF_012932965.1_ASM1293296v1_genomic.fna/tc_result.tsv
[2024-01-24 13:24:36,321] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:36,321] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:36,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd0ff1cf-821d-4019-8f66-aaaa3624e106/dqc_reference/checkm_data
[2024-01-24 13:24:36,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:36,361] [INFO] Task started: CheckM
[2024-01-24 13:24:36,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012932965.1_ASM1293296v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012932965.1_ASM1293296v1_genomic.fna/checkm_input GCF_012932965.1_ASM1293296v1_genomic.fna/checkm_result
[2024-01-24 13:25:04,077] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:04,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:04,096] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:04,096] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:04,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012932965.1_ASM1293296v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:04,097] [INFO] Task started: Blastn
[2024-01-24 13:25:04,097] [INFO] Running command: blastn -query GCF_012932965.1_ASM1293296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd0ff1cf-821d-4019-8f66-aaaa3624e106/dqc_reference/reference_markers_gtdb.fasta -out GCF_012932965.1_ASM1293296v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:05,215] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:05,218] [INFO] Selected 20 target genomes.
[2024-01-24 13:25:05,218] [INFO] Target genome list was writen to GCF_012932965.1_ASM1293296v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:05,256] [INFO] Task started: fastANI
[2024-01-24 13:25:05,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg295e7413-daa7-487d-be02-052db4e693b4/GCF_012932965.1_ASM1293296v1_genomic.fna.gz --refList GCF_012932965.1_ASM1293296v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012932965.1_ASM1293296v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:21,056] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:21,071] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:21,072] [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_012932965.1	s__Thalassotalea algicola	100.0	1347	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003390395.1	s__Thalassotalea euphylliae_C	79.877	349	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390375.1	s__Thalassotalea euphylliae_A	78.9839	328	1349	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	78.6542	312	1349	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	78.5933	175	1349	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	78.3565	166	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111755.1	s__Thalassotalea_D agarivorans	78.3495	136	1349	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_014656435.1	s__Thalassotalea_C marina	78.292	190	1349	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_014653195.1	s__Thalassotalea_B profundi	78.1923	190	1349	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_017168195.1	s__G2M2-11 sp017168195	78.004	195	1349	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_002104515.1	s__Cognaticolwellia polaris	77.7115	199	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	77.6954	191	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843355.2	s__Colwellia echini	77.6953	162	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	77.6438	183	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003333305.1	s__Colwellia aromaticivorans	77.5937	160	1349	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	77.5523	166	1349	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	77.5461	185	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013216015.1	s__JABSOI01 sp013216015	77.4106	145	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215655.1	s__Colwellia_A sp013215655	77.3996	170	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733765.1	s__Colwellia sp002733765	77.3364	158	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:21,074] [INFO] GTDB search result was written to GCF_012932965.1_ASM1293296v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:21,074] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:21,078] [INFO] DFAST_QC result json was written to GCF_012932965.1_ASM1293296v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:21,078] [INFO] DFAST_QC completed!
[2024-01-24 13:25:21,078] [INFO] Total running time: 0h1m8s