[2024-01-24 15:18:38,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,587] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,587] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a463cb9-4ea8-44af-9cff-8d3edd9fa630/dqc_reference
[2024-01-24 15:18:39,889] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:39,890] [INFO] Task started: Prodigal
[2024-01-24 15:18:39,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg136f6250-f8c2-4f3d-9433-19fc8f398a41/GCF_026241225.1_ASM2624122v1_genomic.fna.gz | prodigal -d GCF_026241225.1_ASM2624122v1_genomic.fna/cds.fna -a GCF_026241225.1_ASM2624122v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:54,806] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:54,807] [INFO] Task started: HMMsearch
[2024-01-24 15:18:54,807] [INFO] Running command: hmmsearch --tblout GCF_026241225.1_ASM2624122v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a463cb9-4ea8-44af-9cff-8d3edd9fa630/dqc_reference/reference_markers.hmm GCF_026241225.1_ASM2624122v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:55,088] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:55,089] [INFO] Found 6/6 markers.
[2024-01-24 15:18:55,121] [INFO] Query marker FASTA was written to GCF_026241225.1_ASM2624122v1_genomic.fna/markers.fasta
[2024-01-24 15:18:55,121] [INFO] Task started: Blastn
[2024-01-24 15:18:55,121] [INFO] Running command: blastn -query GCF_026241225.1_ASM2624122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a463cb9-4ea8-44af-9cff-8d3edd9fa630/dqc_reference/reference_markers.fasta -out GCF_026241225.1_ASM2624122v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:55,777] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:55,782] [INFO] Selected 28 target genomes.
[2024-01-24 15:18:55,783] [INFO] Target genome list was writen to GCF_026241225.1_ASM2624122v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:55,795] [INFO] Task started: fastANI
[2024-01-24 15:18:55,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg136f6250-f8c2-4f3d-9433-19fc8f398a41/GCF_026241225.1_ASM2624122v1_genomic.fna.gz --refList GCF_026241225.1_ASM2624122v1_genomic.fna/target_genomes.txt --output GCF_026241225.1_ASM2624122v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:14,246] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:14,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a463cb9-4ea8-44af-9cff-8d3edd9fa630/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:14,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a463cb9-4ea8-44af-9cff-8d3edd9fa630/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:14,263] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:14,263] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:14,264] [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
Muriicola marianensis	strain=CGMCC 1.12606	GCA_014638095.1	1324801	1324801	type	True	77.1309	125	1040	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	76.9989	65	1040	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	76.9409	65	1040	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.8902	116	1040	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	76.8337	71	1040	95	below_threshold
Muriicola jejuensis	strain=KCTC 22299	GCA_010671595.1	504488	504488	type	True	76.8157	110	1040	95	below_threshold
Eudoraea adriatica	strain=DSM 19308	GCA_000382125.1	446681	446681	type	True	76.7781	109	1040	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	76.7337	79	1040	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	76.729	70	1040	95	below_threshold
Zeaxanthinibacter enoshimensis	strain=DSM 18435	GCA_004362865.1	392009	392009	type	True	76.651	103	1040	95	below_threshold
Maribacter arenosus	strain=CAU 1321	GCA_014610845.1	1854708	1854708	type	True	76.5903	69	1040	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	76.5435	66	1040	95	below_threshold
Pareuzebyella sediminis	strain=S2-4-21	GCA_008367235.1	2607998	2607998	type	True	76.5409	62	1040	95	below_threshold
Muricauda algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	76.5114	71	1040	95	below_threshold
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	76.4111	59	1040	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.3719	50	1040	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	76.3667	86	1040	95	below_threshold
Robiginitalea myxolifaciens	strain=DSM 21019	GCA_900115205.1	400055	400055	type	True	76.1808	85	1040	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	76.0998	71	1040	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.0706	74	1040	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	76.0594	72	1040	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:14,265] [INFO] DFAST Taxonomy check result was written to GCF_026241225.1_ASM2624122v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:14,270] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:14,271] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:14,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a463cb9-4ea8-44af-9cff-8d3edd9fa630/dqc_reference/checkm_data
[2024-01-24 15:19:14,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:14,309] [INFO] Task started: CheckM
[2024-01-24 15:19:14,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026241225.1_ASM2624122v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026241225.1_ASM2624122v1_genomic.fna/checkm_input GCF_026241225.1_ASM2624122v1_genomic.fna/checkm_result
[2024-01-24 15:19:59,186] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:59,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:59,209] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:59,209] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:59,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026241225.1_ASM2624122v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:59,210] [INFO] Task started: Blastn
[2024-01-24 15:19:59,210] [INFO] Running command: blastn -query GCF_026241225.1_ASM2624122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a463cb9-4ea8-44af-9cff-8d3edd9fa630/dqc_reference/reference_markers_gtdb.fasta -out GCF_026241225.1_ASM2624122v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:59,969] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:59,973] [INFO] Selected 26 target genomes.
[2024-01-24 15:19:59,974] [INFO] Target genome list was writen to GCF_026241225.1_ASM2624122v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:59,993] [INFO] Task started: fastANI
[2024-01-24 15:19:59,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg136f6250-f8c2-4f3d-9433-19fc8f398a41/GCF_026241225.1_ASM2624122v1_genomic.fna.gz --refList GCF_026241225.1_ASM2624122v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026241225.1_ASM2624122v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:14,242] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:14,261] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:20:14,261] [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
GCA_013041785.1	s__Eudoraea sp013041785	78.2338	214	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Eudoraea	95.0	97.28	95.79	0.83	0.71	4	-
GCF_014638095.1	s__Muriicola marianensis	77.1345	124	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011068285.1	s__Muricauda sp011068285	76.9846	63	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009901585.1	s__R33 sp009901585	76.8902	116	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__R33	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992595.1	s__Muricauda sp002452975	76.8365	70	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCF_000382125.1	s__Eudoraea adriatica	76.7781	109	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Eudoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058265.1	s__Muricauda sp003058265	76.7337	79	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785775.2	s__Muricauda sp003973595	76.729	70	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_001413955.1	s__Muricauda eckloniae	76.6824	59	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003145.1	s__Zeaxanthinibacter sp013003145	76.6717	51	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362865.1	s__Zeaxanthinibacter enoshimensis	76.6511	102	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014610845.1	s__Maribacter_A arenosus	76.5903	69	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	76.5532	78	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_013090115.1	s__Muricauda amphidinii	76.542	65	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008367235.1	s__Pareuzebyella sediminis	76.5409	62	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pareuzebyella	95.0	99.39	99.39	0.97	0.97	2	-
GCF_005937185.1	s__Muricauda algicola	76.5403	70	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042255.1	s__Muriicola sp013042255	76.4578	51	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	98.63	98.55	0.78	0.75	6	-
GCF_003149745.1	s__Muricauda koreensis	76.447	62	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042315.1	s__Muriicola sp013042315	76.4369	73	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	99.31	99.31	0.85	0.85	2	-
GCA_002167435.2	s__Muricauda sp002167435	76.4205	55	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382275.1	s__Muricauda nanhaiensis	76.415	86	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009371985.2	s__TP-CH-4 sp009371985	76.4022	57	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TP-CH-4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699205.1	s__Muricauda sp002699205	76.3824	63	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.91	99.91	0.89	0.89	2	-
GCF_003992615.1	s__Muricauda beolgyonensis	76.3667	86	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:14,263] [INFO] GTDB search result was written to GCF_026241225.1_ASM2624122v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:14,264] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:14,274] [INFO] DFAST_QC result json was written to GCF_026241225.1_ASM2624122v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:14,275] [INFO] DFAST_QC completed!
[2024-01-24 15:20:14,275] [INFO] Total running time: 0h1m36s