[2023-06-30 20:06:56,578] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:06:56,580] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:06:56,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg6911e96b-afda-4ee4-b391-16b85e71b430/dqc_reference
[2023-06-30 20:06:58,211] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:06:58,212] [INFO] Task started: Prodigal
[2023-06-30 20:06:58,212] [INFO] Running command: gunzip -c /var/lib/cwl/stga253517f-233c-4e0c-bbb9-7d2aa0d4e608/GCA_024642005.1_ASM2464200v1_genomic.fna.gz | prodigal -d GCA_024642005.1_ASM2464200v1_genomic.fna/cds.fna -a GCA_024642005.1_ASM2464200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:07:17,734] [INFO] Task succeeded: Prodigal
[2023-06-30 20:07:17,734] [INFO] Task started: HMMsearch
[2023-06-30 20:07:17,734] [INFO] Running command: hmmsearch --tblout GCA_024642005.1_ASM2464200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6911e96b-afda-4ee4-b391-16b85e71b430/dqc_reference/reference_markers.hmm GCA_024642005.1_ASM2464200v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:07:18,067] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:07:18,069] [INFO] Found 6/6 markers.
[2023-06-30 20:07:18,101] [INFO] Query marker FASTA was written to GCA_024642005.1_ASM2464200v1_genomic.fna/markers.fasta
[2023-06-30 20:07:18,102] [INFO] Task started: Blastn
[2023-06-30 20:07:18,102] [INFO] Running command: blastn -query GCA_024642005.1_ASM2464200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6911e96b-afda-4ee4-b391-16b85e71b430/dqc_reference/reference_markers.fasta -out GCA_024642005.1_ASM2464200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:07:18,736] [INFO] Task succeeded: Blastn
[2023-06-30 20:07:18,740] [INFO] Selected 25 target genomes.
[2023-06-30 20:07:18,740] [INFO] Target genome list was writen to GCA_024642005.1_ASM2464200v1_genomic.fna/target_genomes.txt
[2023-06-30 20:07:18,742] [INFO] Task started: fastANI
[2023-06-30 20:07:18,743] [INFO] Running command: fastANI --query /var/lib/cwl/stga253517f-233c-4e0c-bbb9-7d2aa0d4e608/GCA_024642005.1_ASM2464200v1_genomic.fna.gz --refList GCA_024642005.1_ASM2464200v1_genomic.fna/target_genomes.txt --output GCA_024642005.1_ASM2464200v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:07:34,774] [INFO] Task succeeded: fastANI
[2023-06-30 20:07:34,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6911e96b-afda-4ee4-b391-16b85e71b430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:07:34,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6911e96b-afda-4ee4-b391-16b85e71b430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:07:34,790] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:07:34,790] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 20:07:34,791] [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
Robiginitalea sediminis	strain=O458	GCA_002198115.1	1982593	1982593	type	True	77.573	325	1105	95	below_threshold
Robiginitalea biformata	strain=HTCC2501	GCA_000024125.1	252307	252307	type	True	77.5059	318	1105	95	below_threshold
Robiginitalea myxolifaciens	strain=DSM 21019	GCA_900115205.1	400055	400055	type	True	76.9605	115	1105	95	below_threshold
Muriicola jejuensis	strain=KCTC 22299	GCA_010671595.1	504488	504488	type	True	76.5729	114	1105	95	below_threshold
Muriicola soli	strain=MMS17-SY002	GCA_004139715.1	2507538	2507538	type	True	76.3274	51	1105	95	below_threshold
Muriicola marianensis	strain=CGMCC 1.12606	GCA_014638095.1	1324801	1324801	type	True	76.1581	116	1105	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	76.136	74	1105	95	below_threshold
Sinomicrobium kalidii	strain=HD2P242	GCA_021183825.1	2900738	2900738	type	True	76.1057	51	1105	95	below_threshold
Muricauda antarctica	strain=CGMCC 1.12174	GCA_900142405.1	1055723	1055723	type	True	76.067	73	1105	95	below_threshold
Muricauda antarctica	strain=DSM 26351	GCA_900112295.1	1055723	1055723	type	True	76.0626	72	1105	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	76.0281	65	1105	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	75.9157	75	1105	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	75.6736	56	1105	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	75.6736	56	1105	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:07:34,793] [INFO] DFAST Taxonomy check result was written to GCA_024642005.1_ASM2464200v1_genomic.fna/tc_result.tsv
[2023-06-30 20:07:34,793] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:07:34,793] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:07:34,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6911e96b-afda-4ee4-b391-16b85e71b430/dqc_reference/checkm_data
[2023-06-30 20:07:34,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:07:34,836] [INFO] Task started: CheckM
[2023-06-30 20:07:34,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024642005.1_ASM2464200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024642005.1_ASM2464200v1_genomic.fna/checkm_input GCA_024642005.1_ASM2464200v1_genomic.fna/checkm_result
[2023-06-30 20:08:27,497] [INFO] Task succeeded: CheckM
[2023-06-30 20:08:27,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:08:27,523] [INFO] ===== Completeness check finished =====
[2023-06-30 20:08:27,523] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:08:27,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024642005.1_ASM2464200v1_genomic.fna/markers.fasta)
[2023-06-30 20:08:27,524] [INFO] Task started: Blastn
[2023-06-30 20:08:27,524] [INFO] Running command: blastn -query GCA_024642005.1_ASM2464200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6911e96b-afda-4ee4-b391-16b85e71b430/dqc_reference/reference_markers_gtdb.fasta -out GCA_024642005.1_ASM2464200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:08:28,294] [INFO] Task succeeded: Blastn
[2023-06-30 20:08:28,299] [INFO] Selected 22 target genomes.
[2023-06-30 20:08:28,299] [INFO] Target genome list was writen to GCA_024642005.1_ASM2464200v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:08:28,311] [INFO] Task started: fastANI
[2023-06-30 20:08:28,311] [INFO] Running command: fastANI --query /var/lib/cwl/stga253517f-233c-4e0c-bbb9-7d2aa0d4e608/GCA_024642005.1_ASM2464200v1_genomic.fna.gz --refList GCA_024642005.1_ASM2464200v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024642005.1_ASM2464200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:08:39,228] [INFO] Task succeeded: fastANI
[2023-06-30 20:08:39,244] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 20:08:39,245] [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_014243345.1	s__Robiginitalea sp014243345	77.6468	362	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198115.1	s__Robiginitalea sediminis	77.573	325	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024125.1	s__Robiginitalea biformata	77.5059	318	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115205.1	s__Robiginitalea myxolifaciens	76.9605	115	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001683825.1	s__Zeaxanthinibacter sp001683825	76.4352	144	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214065.1	s__DT-32 sp013214065	76.3771	54	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__DT-32	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638095.1	s__Muriicola marianensis	76.151	115	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058265.1	s__Muricauda sp003058265	76.136	74	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584105.1	s__Muricauda taeanensis	76.0281	65	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_003285545.1	s__Sinomicrobium sp003285545	76.0094	60	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407935.1	s__Muricauda sp013407935	75.9452	52	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.58	96.50	0.87	0.86	8	-
GCF_009184425.1	s__Muricauda olearia	75.9381	59	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_007785775.2	s__Muricauda sp003973595	75.935	74	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-30 20:08:39,247] [INFO] GTDB search result was written to GCA_024642005.1_ASM2464200v1_genomic.fna/result_gtdb.tsv
[2023-06-30 20:08:39,248] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:08:39,252] [INFO] DFAST_QC result json was written to GCA_024642005.1_ASM2464200v1_genomic.fna/dqc_result.json
[2023-06-30 20:08:39,252] [INFO] DFAST_QC completed!
[2023-06-30 20:08:39,252] [INFO] Total running time: 0h1m43s