[2024-01-24 13:57:57,103] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:57,107] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:57,107] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b5379ea-60f9-4303-8599-b2a081e11c9d/dqc_reference
[2024-01-24 13:57:58,451] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:58,452] [INFO] Task started: Prodigal
[2024-01-24 13:57:58,452] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e733d7c-3977-411e-9110-0086d79ecd87/GCF_027474845.2_ASM2747484v2_genomic.fna.gz | prodigal -d GCF_027474845.2_ASM2747484v2_genomic.fna/cds.fna -a GCF_027474845.2_ASM2747484v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:16,009] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:16,010] [INFO] Task started: HMMsearch
[2024-01-24 13:58:16,010] [INFO] Running command: hmmsearch --tblout GCF_027474845.2_ASM2747484v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b5379ea-60f9-4303-8599-b2a081e11c9d/dqc_reference/reference_markers.hmm GCF_027474845.2_ASM2747484v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:16,293] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:16,295] [INFO] Found 6/6 markers.
[2024-01-24 13:58:16,327] [INFO] Query marker FASTA was written to GCF_027474845.2_ASM2747484v2_genomic.fna/markers.fasta
[2024-01-24 13:58:16,328] [INFO] Task started: Blastn
[2024-01-24 13:58:16,328] [INFO] Running command: blastn -query GCF_027474845.2_ASM2747484v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b5379ea-60f9-4303-8599-b2a081e11c9d/dqc_reference/reference_markers.fasta -out GCF_027474845.2_ASM2747484v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:17,049] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:17,052] [INFO] Selected 29 target genomes.
[2024-01-24 13:58:17,052] [INFO] Target genome list was writen to GCF_027474845.2_ASM2747484v2_genomic.fna/target_genomes.txt
[2024-01-24 13:58:17,151] [INFO] Task started: fastANI
[2024-01-24 13:58:17,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e733d7c-3977-411e-9110-0086d79ecd87/GCF_027474845.2_ASM2747484v2_genomic.fna.gz --refList GCF_027474845.2_ASM2747484v2_genomic.fna/target_genomes.txt --output GCF_027474845.2_ASM2747484v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:37,384] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:37,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b5379ea-60f9-4303-8599-b2a081e11c9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:37,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b5379ea-60f9-4303-8599-b2a081e11c9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:37,407] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:37,407] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:37,407] [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
Croceitalea dokdonensis	strain=DOKDO 023	GCA_001306415.1	346188	346188	type	True	79.6963	113	1288	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	78.2583	210	1288	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	78.0162	207	1288	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	77.704	201	1288	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	77.6987	243	1288	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	77.6913	213	1288	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	77.6162	215	1288	95	below_threshold
Maribacter aurantiacus	strain=KCTC 52409	GCA_005780245.1	1882343	1882343	type	True	77.5117	192	1288	95	below_threshold
Maribacter antarcticus	strain=DSM 21422	GCA_000621125.1	505250	505250	type	True	77.4535	214	1288	95	below_threshold
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	77.4312	206	1288	95	below_threshold
Costertonia aggregata	strain=KCCM 42265	GCA_013402795.1	343403	343403	type	True	77.3086	174	1288	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	77.2481	121	1288	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	77.2477	128	1288	95	below_threshold
Aggregatimonas sangjinii	strain=F202Z8	GCA_005943945.1	2583587	2583587	type	True	77.2291	129	1288	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	77.213	224	1288	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	77.1551	205	1288	95	below_threshold
Zobellia nedashkovskayae	strain=Asnod2-B07-B	GCA_015330125.1	2779510	2779510	type	True	77.1297	141	1288	95	below_threshold
Kriegella aquimaris	strain=DSM 19886	GCA_900103215.1	192904	192904	type	True	77.0422	142	1288	95	below_threshold
Maribacter arenosus	strain=CAU 1321	GCA_014610845.1	1854708	1854708	type	True	77.0109	150	1288	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	76.841	118	1288	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.7864	140	1288	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	76.767	97	1288	95	below_threshold
Arenibacter hampyeongensis	strain=JCM 17788	GCA_002909255.1	1028743	1028743	type	True	76.7654	116	1288	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	76.5649	118	1288	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	76.5142	129	1288	95	below_threshold
Euzebyella saccharophila	strain=7SM30	GCA_014855495.1	679664	679664	type	True	76.4568	144	1288	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	76.4213	92	1288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:37,410] [INFO] DFAST Taxonomy check result was written to GCF_027474845.2_ASM2747484v2_genomic.fna/tc_result.tsv
[2024-01-24 13:58:37,411] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:37,411] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:37,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b5379ea-60f9-4303-8599-b2a081e11c9d/dqc_reference/checkm_data
[2024-01-24 13:58:37,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:37,455] [INFO] Task started: CheckM
[2024-01-24 13:58:37,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027474845.2_ASM2747484v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027474845.2_ASM2747484v2_genomic.fna/checkm_input GCF_027474845.2_ASM2747484v2_genomic.fna/checkm_result
[2024-01-24 13:59:27,058] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:27,060] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:27,079] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:27,079] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:27,080] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027474845.2_ASM2747484v2_genomic.fna/markers.fasta)
[2024-01-24 13:59:27,080] [INFO] Task started: Blastn
[2024-01-24 13:59:27,080] [INFO] Running command: blastn -query GCF_027474845.2_ASM2747484v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b5379ea-60f9-4303-8599-b2a081e11c9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_027474845.2_ASM2747484v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:27,953] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:27,958] [INFO] Selected 28 target genomes.
[2024-01-24 13:59:27,958] [INFO] Target genome list was writen to GCF_027474845.2_ASM2747484v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:28,116] [INFO] Task started: fastANI
[2024-01-24 13:59:28,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e733d7c-3977-411e-9110-0086d79ecd87/GCF_027474845.2_ASM2747484v2_genomic.fna.gz --refList GCF_027474845.2_ASM2747484v2_genomic.fna/target_genomes_gtdb.txt --output GCF_027474845.2_ASM2747484v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:47,793] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:47,817] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:47,818] [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_905479535.1	s__Maribacter sp905479535	81.8106	459	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970695.1	s__Maribacter sp002742365	78.8052	344	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.61	96.61	0.86	0.86	2	-
GCF_003075045.1	s__Maribacter litoralis	78.2583	210	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_009674825.1	s__Maribacter_A luteus	77.986	168	1288	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_018100785.1	s__Maribacter sp018100785	77.8851	224	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744105.1	s__Maribacter forsetii	77.7094	200	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109345.1	s__Maribacter orientalis	77.7066	212	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001020565.1	s__Maribacter thermophilus	77.6987	243	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167935.1	s__Maribacter arcticus	77.6162	215	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621125.1	s__Maribacter antarcticus	77.5299	215	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386635.1	s__Maribacter flavus	77.4312	206	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.59	96.59	0.88	0.88	2	-
GCF_013402795.1	s__Costertonia aggregata	77.3686	174	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Costertonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	77.3214	195	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900112245.1	s__Maribacter stanieri	77.2155	223	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_003269425.1	s__Muricauda maritima	77.1673	128	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005943945.1	s__F202Z8 sp005943945	77.1512	129	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__F202Z8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015330125.1	s__Zobellia sp015330125	77.1297	141	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.92	0.92	2	-
GCF_000224085.1	s__Muricauda ruestringensis	77.0732	99	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581615.1	s__Muricauda lutimaris	77.0561	118	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103215.1	s__Kriegella aquimaris	77.0422	142	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kriegella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014610845.1	s__Maribacter_A arenosus	77.028	149	1288	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_002909255.1	s__Arenibacter hampyeongensis	76.7654	116	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129275.1	s__Arenibacter palladensis	76.6408	127	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
GCF_018860365.1	s__Arenibacter algicola_B	76.6067	133	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745185.1	s__Muricauda sp000745185	76.5918	101	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177645.1	s__Arenibacter troitsensis	76.5795	118	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141935.1	s__Arenibacter nanhaiticus	76.4948	87	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167435.2	s__Muricauda sp002167435	76.444	104	1288	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 13:59:47,820] [INFO] GTDB search result was written to GCF_027474845.2_ASM2747484v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:47,821] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:47,827] [INFO] DFAST_QC result json was written to GCF_027474845.2_ASM2747484v2_genomic.fna/dqc_result.json
[2024-01-24 13:59:47,828] [INFO] DFAST_QC completed!
[2024-01-24 13:59:47,828] [INFO] Total running time: 0h1m51s