[2024-01-25 18:51:35,842] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:35,844] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:35,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d5235be-4048-4b2e-9039-2cb45c3228ec/dqc_reference
[2024-01-25 18:51:37,037] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:37,038] [INFO] Task started: Prodigal
[2024-01-25 18:51:37,038] [INFO] Running command: gunzip -c /var/lib/cwl/stg22c6b18b-6f92-4c3f-9aba-75d6f3d23537/GCF_011074955.1_ASM1107495v1_genomic.fna.gz | prodigal -d GCF_011074955.1_ASM1107495v1_genomic.fna/cds.fna -a GCF_011074955.1_ASM1107495v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:48,755] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:48,755] [INFO] Task started: HMMsearch
[2024-01-25 18:51:48,755] [INFO] Running command: hmmsearch --tblout GCF_011074955.1_ASM1107495v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d5235be-4048-4b2e-9039-2cb45c3228ec/dqc_reference/reference_markers.hmm GCF_011074955.1_ASM1107495v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:49,058] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:49,059] [INFO] Found 6/6 markers.
[2024-01-25 18:51:49,101] [INFO] Query marker FASTA was written to GCF_011074955.1_ASM1107495v1_genomic.fna/markers.fasta
[2024-01-25 18:51:49,101] [INFO] Task started: Blastn
[2024-01-25 18:51:49,101] [INFO] Running command: blastn -query GCF_011074955.1_ASM1107495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d5235be-4048-4b2e-9039-2cb45c3228ec/dqc_reference/reference_markers.fasta -out GCF_011074955.1_ASM1107495v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:49,883] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:49,886] [INFO] Selected 23 target genomes.
[2024-01-25 18:51:49,886] [INFO] Target genome list was writen to GCF_011074955.1_ASM1107495v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:49,898] [INFO] Task started: fastANI
[2024-01-25 18:51:49,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg22c6b18b-6f92-4c3f-9aba-75d6f3d23537/GCF_011074955.1_ASM1107495v1_genomic.fna.gz --refList GCF_011074955.1_ASM1107495v1_genomic.fna/target_genomes.txt --output GCF_011074955.1_ASM1107495v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:06,154] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:06,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d5235be-4048-4b2e-9039-2cb45c3228ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:06,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d5235be-4048-4b2e-9039-2cb45c3228ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:06,167] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:52:06,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:06,168] [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
Marinobacter caseinilyticus	strain=M3-13	GCA_011074955.1	2692195	2692195	type	True	100.0	1414	1418	95	conclusive
Marinobacter changyiensis	strain=CLL7-20	GCA_009193265.1	2604091	2604091	type	True	79.5916	461	1418	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	78.5434	307	1418	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	78.4781	335	1418	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_012956055.1	1928859	1928859	type	True	78.4771	296	1418	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	78.2216	307	1418	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	78.137	270	1418	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	78.105	285	1418	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	78.0059	300	1418	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	77.9958	250	1418	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	77.9794	302	1418	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	77.9745	333	1418	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	77.9292	329	1418	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	77.8952	260	1418	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	77.8808	283	1418	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	77.8796	353	1418	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	77.855	204	1418	95	below_threshold
Marinobacter zhejiangensis	strain=CGMCC 1.7061	GCA_900114775.1	488535	488535	type	True	77.7756	253	1418	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	77.7541	292	1418	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	77.5856	301	1418	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	77.5751	283	1418	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	75.9743	66	1418	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:06,169] [INFO] DFAST Taxonomy check result was written to GCF_011074955.1_ASM1107495v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:06,169] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:06,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:06,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d5235be-4048-4b2e-9039-2cb45c3228ec/dqc_reference/checkm_data
[2024-01-25 18:52:06,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:06,211] [INFO] Task started: CheckM
[2024-01-25 18:52:06,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011074955.1_ASM1107495v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011074955.1_ASM1107495v1_genomic.fna/checkm_input GCF_011074955.1_ASM1107495v1_genomic.fna/checkm_result
[2024-01-25 18:52:42,220] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:42,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:42,236] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:42,236] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:42,237] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011074955.1_ASM1107495v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:42,237] [INFO] Task started: Blastn
[2024-01-25 18:52:42,237] [INFO] Running command: blastn -query GCF_011074955.1_ASM1107495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d5235be-4048-4b2e-9039-2cb45c3228ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_011074955.1_ASM1107495v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:43,537] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:43,540] [INFO] Selected 24 target genomes.
[2024-01-25 18:52:43,540] [INFO] Target genome list was writen to GCF_011074955.1_ASM1107495v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:43,557] [INFO] Task started: fastANI
[2024-01-25 18:52:43,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg22c6b18b-6f92-4c3f-9aba-75d6f3d23537/GCF_011074955.1_ASM1107495v1_genomic.fna.gz --refList GCF_011074955.1_ASM1107495v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011074955.1_ASM1107495v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:01,087] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:01,101] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:53:01,101] [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_011074955.1	s__Marinobacter caseinilyticus	100.0	1415	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009193265.1	s__Marinobacter changyiensis	79.5976	460	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005298175.1	s__Marinobacter sp005298175	78.7306	334	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170835.1	s__Marinobacter algicola	78.5487	307	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003441595.1	s__Marinobacter sp003441595	78.2184	325	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994855.1	s__Marinobacter sp003994855	78.2072	346	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188315.1	s__Marinobacter sp900188315	78.1446	293	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.8497	N/A	N/A	N/A	N/A	1	-
GCF_008107725.1	s__Marinobacter sp008107725	78.1394	299	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	78.123	271	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_005871205.1	s__Marinobacter alexandrii	78.1178	320	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.69	98.69	0.90	0.90	2	-
GCF_001447155.2	s__Marinobacter sp001447155	78.1079	280	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792665.1	s__Marinobacter orientalis	78.1026	287	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000686085.1	s__Marinobacter sp000686085	78.0925	342	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000397065.2	s__Marinobacter lipolyticus	78.0499	305	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007675.1	s__Marinobacter fuscus	77.9917	249	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007685.1	s__Marinobacter halophilus	77.9781	260	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000284615.1	s__Marinobacter hydrocarbonoclasticus	77.9653	275	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCF_016820575.1	s__Marinobacter sediminum	77.9269	330	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744715.1	s__Marinobacter profundi	77.8895	352	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCF_003344045.1	s__Marinobacter vulgaris	77.8752	294	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003007715.1	s__Marinobacter shengliensis	77.7475	292	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	-
GCF_014201735.1	s__Marinobacter oulmenensis	77.6527	221	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859525.1	s__Marinobacter sp014859525	77.5801	226	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427555.1	s__Marinobacter litoralis_A	77.5594	212	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:53:01,102] [INFO] GTDB search result was written to GCF_011074955.1_ASM1107495v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:01,103] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:01,107] [INFO] DFAST_QC result json was written to GCF_011074955.1_ASM1107495v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:01,107] [INFO] DFAST_QC completed!
[2024-01-25 18:53:01,107] [INFO] Total running time: 0h1m25s