[2024-01-25 18:11:35,447] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:35,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:35,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg0641579b-a2cf-4cd4-9c00-408d8e349930/dqc_reference
[2024-01-25 18:11:36,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:36,674] [INFO] Task started: Prodigal
[2024-01-25 18:11:36,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg785ab26b-6cec-43f3-8a27-05b645bf616a/GCF_023051175.1_ASM2305117v1_genomic.fna.gz | prodigal -d GCF_023051175.1_ASM2305117v1_genomic.fna/cds.fna -a GCF_023051175.1_ASM2305117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:46,127] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:46,127] [INFO] Task started: HMMsearch
[2024-01-25 18:11:46,127] [INFO] Running command: hmmsearch --tblout GCF_023051175.1_ASM2305117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0641579b-a2cf-4cd4-9c00-408d8e349930/dqc_reference/reference_markers.hmm GCF_023051175.1_ASM2305117v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:46,338] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:46,339] [INFO] Found 6/6 markers.
[2024-01-25 18:11:46,367] [INFO] Query marker FASTA was written to GCF_023051175.1_ASM2305117v1_genomic.fna/markers.fasta
[2024-01-25 18:11:46,367] [INFO] Task started: Blastn
[2024-01-25 18:11:46,367] [INFO] Running command: blastn -query GCF_023051175.1_ASM2305117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0641579b-a2cf-4cd4-9c00-408d8e349930/dqc_reference/reference_markers.fasta -out GCF_023051175.1_ASM2305117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:47,197] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:47,200] [INFO] Selected 19 target genomes.
[2024-01-25 18:11:47,200] [INFO] Target genome list was writen to GCF_023051175.1_ASM2305117v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:47,224] [INFO] Task started: fastANI
[2024-01-25 18:11:47,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg785ab26b-6cec-43f3-8a27-05b645bf616a/GCF_023051175.1_ASM2305117v1_genomic.fna.gz --refList GCF_023051175.1_ASM2305117v1_genomic.fna/target_genomes.txt --output GCF_023051175.1_ASM2305117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:01,177] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:01,177] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0641579b-a2cf-4cd4-9c00-408d8e349930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:01,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0641579b-a2cf-4cd4-9c00-408d8e349930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:01,188] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:12:01,188] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:12:01,189] [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
Alcanivorax pacificus	strain=W11-5	GCA_000299335.2	1306787	1306787	type	True	80.1204	625	1059	95	below_threshold
Alcanivorax indicus	strain=SW127	GCA_003259185.1	2202653	2202653	type	True	78.3988	392	1059	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	78.1895	345	1059	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	77.7765	249	1059	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	77.7026	256	1059	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	77.5816	247	1059	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	77.4763	272	1059	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	77.4433	222	1059	95	below_threshold
Alcanivorax dieselolei	strain=CGMCC 1.3690	GCA_014644575.1	285091	285091	type	True	77.161	223	1059	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	77.1555	254	1059	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	76.4724	149	1059	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	76.394	123	1059	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	76.2129	103	1059	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	76.1707	68	1059	95	below_threshold
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	76.1013	95	1059	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	75.9489	81	1059	95	below_threshold
Natronospirillum operosum	strain=G-116	GCA_004768465.1	2759953	2759953	type	True	75.8302	74	1059	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:01,190] [INFO] DFAST Taxonomy check result was written to GCF_023051175.1_ASM2305117v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:01,191] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:01,191] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:01,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0641579b-a2cf-4cd4-9c00-408d8e349930/dqc_reference/checkm_data
[2024-01-25 18:12:01,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:01,225] [INFO] Task started: CheckM
[2024-01-25 18:12:01,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023051175.1_ASM2305117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023051175.1_ASM2305117v1_genomic.fna/checkm_input GCF_023051175.1_ASM2305117v1_genomic.fna/checkm_result
[2024-01-25 18:12:32,091] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:32,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:32,118] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:32,118] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:32,119] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023051175.1_ASM2305117v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:32,120] [INFO] Task started: Blastn
[2024-01-25 18:12:32,120] [INFO] Running command: blastn -query GCF_023051175.1_ASM2305117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0641579b-a2cf-4cd4-9c00-408d8e349930/dqc_reference/reference_markers_gtdb.fasta -out GCF_023051175.1_ASM2305117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:33,683] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:33,686] [INFO] Selected 19 target genomes.
[2024-01-25 18:12:33,686] [INFO] Target genome list was writen to GCF_023051175.1_ASM2305117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:33,712] [INFO] Task started: fastANI
[2024-01-25 18:12:33,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg785ab26b-6cec-43f3-8a27-05b645bf616a/GCF_023051175.1_ASM2305117v1_genomic.fna.gz --refList GCF_023051175.1_ASM2305117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023051175.1_ASM2305117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:46,772] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:46,784] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:12:46,785] [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_000299335.2	s__Alcanivorax_A pacificus	80.1205	625	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846755.1	s__Alcanivorax_A sp009846755	80.0201	589	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823245.1	s__Alcanivorax_A sp013823245	78.4037	343	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259185.1	s__Alcanivorax_A indicus	78.3983	392	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265435.1	s__Alcanivorax profundimaris	77.7895	248	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_015356855.1	s__Alcanivorax venustensis	77.7157	255	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	-
GCF_016906305.1	s__Alcanivorax marinus_B	77.5583	265	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785095.1	s__Alcanivorax marinus_A	77.4842	253	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	77.4764	272	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCF_000300995.1	s__Alcanivorax hongdengensis	77.4433	222	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794945.1	s__Alcanivorax sp009711585	77.3907	216	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	-
GCF_000155615.1	s__Alcanivorax sp000155615	77.1823	180	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.69	0.92	0.89	4	-
GCF_002864685.1	s__Alcanivorax mobilis	77.1548	254	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.57	98.57	0.96	0.96	2	-
GCF_009601165.1	s__Alcanivorax sediminis	77.1133	172	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726155.1	s__Alcanivorax sp002726155	76.8797	165	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100495.1	s__Pseudomonas_E benzenivorans	76.4724	149	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377905.1	s__Thioalkalivibrio sp000377905	76.3219	54	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014931605.1	s__Halomonas sp014931605	76.3149	82	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645095.1	s__Halomonas_F sp015645095	76.049	103	1059	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:46,786] [INFO] GTDB search result was written to GCF_023051175.1_ASM2305117v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:46,787] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:46,791] [INFO] DFAST_QC result json was written to GCF_023051175.1_ASM2305117v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:46,791] [INFO] DFAST_QC completed!
[2024-01-25 18:12:46,791] [INFO] Total running time: 0h1m11s