[2024-01-25 18:48:05,492] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:05,495] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:05,495] [INFO] DQC Reference Directory: /var/lib/cwl/stg11b23cb8-943b-4ef5-80c6-56b9c5248033/dqc_reference
[2024-01-25 18:48:06,657] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:06,658] [INFO] Task started: Prodigal
[2024-01-25 18:48:06,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg57bcf82d-b6a7-4a3b-b1aa-9489f0812ce2/GCF_021245805.1_ASM2124580v1_genomic.fna.gz | prodigal -d GCF_021245805.1_ASM2124580v1_genomic.fna/cds.fna -a GCF_021245805.1_ASM2124580v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:19,171] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:19,172] [INFO] Task started: HMMsearch
[2024-01-25 18:48:19,172] [INFO] Running command: hmmsearch --tblout GCF_021245805.1_ASM2124580v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11b23cb8-943b-4ef5-80c6-56b9c5248033/dqc_reference/reference_markers.hmm GCF_021245805.1_ASM2124580v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:19,440] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:19,441] [INFO] Found 6/6 markers.
[2024-01-25 18:48:19,475] [INFO] Query marker FASTA was written to GCF_021245805.1_ASM2124580v1_genomic.fna/markers.fasta
[2024-01-25 18:48:19,475] [INFO] Task started: Blastn
[2024-01-25 18:48:19,475] [INFO] Running command: blastn -query GCF_021245805.1_ASM2124580v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11b23cb8-943b-4ef5-80c6-56b9c5248033/dqc_reference/reference_markers.fasta -out GCF_021245805.1_ASM2124580v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:20,147] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:20,151] [INFO] Selected 34 target genomes.
[2024-01-25 18:48:20,151] [INFO] Target genome list was writen to GCF_021245805.1_ASM2124580v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:20,188] [INFO] Task started: fastANI
[2024-01-25 18:48:20,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg57bcf82d-b6a7-4a3b-b1aa-9489f0812ce2/GCF_021245805.1_ASM2124580v1_genomic.fna.gz --refList GCF_021245805.1_ASM2124580v1_genomic.fna/target_genomes.txt --output GCF_021245805.1_ASM2124580v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:48:39,550] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:39,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11b23cb8-943b-4ef5-80c6-56b9c5248033/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:48:39,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11b23cb8-943b-4ef5-80c6-56b9c5248033/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:48:39,568] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:48:39,568] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:48:39,568] [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
Mangrovimonas xylaniphaga	strain=ST2L12	GCA_001280435.1	1645915	1645915	type	True	77.6283	220	1211	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.5061	209	1211	95	below_threshold
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	77.4998	204	1211	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.4468	190	1211	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.4348	142	1211	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.3654	174	1211	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	77.3505	184	1211	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	77.3103	133	1211	95	below_threshold
Snuella sedimenti	strain=CAU 1569	GCA_016428595.1	2798802	2798802	type	True	77.2002	120	1211	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.1981	130	1211	95	below_threshold
Aurantibacter aestuarii	strain=KCTC 32269	GCA_003008425.1	1266046	1266046	type	True	77.1763	122	1211	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.1657	135	1211	95	below_threshold
Seonamhaeicola aphaedonensis	strain=CECT 8487	GCA_003386195.1	1461338	1461338	type	True	77.1379	136	1211	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.1291	137	1211	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.1218	191	1211	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	77.1214	173	1211	95	below_threshold
Kordia zhangzhouensis	strain=MCCC 1A00726	GCA_001005305.1	1620405	1620405	type	True	77.015	95	1211	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	77.0118	132	1211	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.999	145	1211	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	76.9777	150	1211	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.9296	143	1211	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	76.9251	156	1211	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	76.9085	147	1211	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.8508	178	1211	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.8046	156	1211	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.8046	156	1211	95	below_threshold
Gelidibacter algens	strain=ACAM 536	GCA_001678675.1	49280	49280	type	True	76.7786	122	1211	95	below_threshold
Gelidibacter algens	strain=DSM 12408	GCA_003259265.1	49280	49280	type	True	76.778	125	1211	95	below_threshold
Aestuariivivens sediminicola	strain=MTV5-3	GCA_022662015.1	2913560	2913560	type	True	76.6615	82	1211	95	below_threshold
Gelidibacter mesophilus	strain=DSM 14095	GCA_000423005.1	169050	169050	type	True	76.6485	107	1211	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.4971	95	1211	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	76.4109	77	1211	95	below_threshold
Flavobacterium indicum	strain=GPTSA100-9	GCA_000455605.1	312277	312277	type	True	76.3034	72	1211	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:48:39,570] [INFO] DFAST Taxonomy check result was written to GCF_021245805.1_ASM2124580v1_genomic.fna/tc_result.tsv
[2024-01-25 18:48:39,571] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:48:39,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:48:39,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11b23cb8-943b-4ef5-80c6-56b9c5248033/dqc_reference/checkm_data
[2024-01-25 18:48:39,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:48:39,610] [INFO] Task started: CheckM
[2024-01-25 18:48:39,610] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021245805.1_ASM2124580v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021245805.1_ASM2124580v1_genomic.fna/checkm_input GCF_021245805.1_ASM2124580v1_genomic.fna/checkm_result
[2024-01-25 18:49:17,750] [INFO] Task succeeded: CheckM
[2024-01-25 18:49:17,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:49:17,767] [INFO] ===== Completeness check finished =====
[2024-01-25 18:49:17,768] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:49:17,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021245805.1_ASM2124580v1_genomic.fna/markers.fasta)
[2024-01-25 18:49:17,768] [INFO] Task started: Blastn
[2024-01-25 18:49:17,768] [INFO] Running command: blastn -query GCF_021245805.1_ASM2124580v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11b23cb8-943b-4ef5-80c6-56b9c5248033/dqc_reference/reference_markers_gtdb.fasta -out GCF_021245805.1_ASM2124580v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:18,723] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:18,728] [INFO] Selected 29 target genomes.
[2024-01-25 18:49:18,728] [INFO] Target genome list was writen to GCF_021245805.1_ASM2124580v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:49:18,753] [INFO] Task started: fastANI
[2024-01-25 18:49:18,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg57bcf82d-b6a7-4a3b-b1aa-9489f0812ce2/GCF_021245805.1_ASM2124580v1_genomic.fna.gz --refList GCF_021245805.1_ASM2124580v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021245805.1_ASM2124580v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:49:39,197] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:39,214] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:49:39,214] [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_001280515.1	s__Mangrovimonas sp001280515	96.8622	1044	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	96.69	96.69	0.89	0.89	2	conclusive
GCF_001280505.1	s__Mangrovimonas_A sp001280505	77.6575	211	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280435.1	s__Mangrovimonas_A xylaniphaga	77.6284	220	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas_A	95.0	96.35	96.35	0.93	0.93	2	-
GCF_003944795.1	s__Mangrovimonas spongiae	77.4998	204	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002895005.1	s__Hanstruepera neustonica	77.4927	210	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hanstruepera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348685.1	s__Xanthomarina gelatinilytica	77.3654	174	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	98.37	98.31	0.90	0.88	4	-
GCF_012931685.1	s__Pseudobizionia ponticola	77.3344	185	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudobizionia	95.0	97.35	97.35	0.92	0.92	2	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.2859	206	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_014641635.1	s__Aquaticitalea lipolytica	77.2429	138	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115185.1	s__Algorimicrobium echini	77.2286	160	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	97.77	97.77	0.81	0.81	2	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	77.2154	152	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	77.1893	122	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008425.1	s__Aurantibacter aestuarii	77.1763	122	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	77.1477	136	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_008086165.1	s__Algorimicrobium algoritergicola	77.1214	173	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008084905.1	s__Xanthomarina maritima	77.1211	196	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011777505.1	s__CAU-1491 sp011777505	77.0486	131	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642835.1	s__Tamlana_A agarivorans	77.038	144	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	95.46	95.44	0.83	0.81	3	-
GCF_000427335.1	s__Winogradskyella psychrotolerans	77.0118	132	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973595.1	s__Jejuia pallidilutea	77.007	143	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	98.03	97.97	0.83	0.83	4	-
GCF_009741275.1	s__Winogradskyella endarachnes	76.999	145	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762485.1	s__Yeosuana marina	76.9777	150	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806995.1	s__Confluentibacter lentus	76.9108	157	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006974145.1	s__Changchengzhania lutea	76.9085	147	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Changchengzhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418105.1	s__Oceanihabitans himadriensis	76.8524	177	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280395.1	s__Confluentibacter sp002280395	76.8301	89	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678675.1	s__Gelidibacter algens	76.7786	122	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	99.95	99.95	0.98	0.98	2	-
GCA_018067265.1	s__Oceanihabitans sp018067265	76.6515	121	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455605.1	s__Flavobacterium indicum	76.3034	72	1211	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:49:39,216] [INFO] GTDB search result was written to GCF_021245805.1_ASM2124580v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:49:39,216] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:49:39,221] [INFO] DFAST_QC result json was written to GCF_021245805.1_ASM2124580v1_genomic.fna/dqc_result.json
[2024-01-25 18:49:39,221] [INFO] DFAST_QC completed!
[2024-01-25 18:49:39,221] [INFO] Total running time: 0h1m34s