[2024-01-24 12:13:29,008] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:29,012] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:29,013] [INFO] DQC Reference Directory: /var/lib/cwl/stga4693a93-52f5-4eab-ad64-8c16d91a400a/dqc_reference
[2024-01-24 12:13:30,446] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,447] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,447] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3913057-03dd-46ad-931b-bc8c7ba9c4d8/GCF_006974145.1_ASM697414v1_genomic.fna.gz | prodigal -d GCF_006974145.1_ASM697414v1_genomic.fna/cds.fna -a GCF_006974145.1_ASM697414v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:45,379] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:45,380] [INFO] Task started: HMMsearch
[2024-01-24 12:13:45,380] [INFO] Running command: hmmsearch --tblout GCF_006974145.1_ASM697414v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4693a93-52f5-4eab-ad64-8c16d91a400a/dqc_reference/reference_markers.hmm GCF_006974145.1_ASM697414v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:45,723] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:45,724] [INFO] Found 6/6 markers.
[2024-01-24 12:13:45,765] [INFO] Query marker FASTA was written to GCF_006974145.1_ASM697414v1_genomic.fna/markers.fasta
[2024-01-24 12:13:45,766] [INFO] Task started: Blastn
[2024-01-24 12:13:45,766] [INFO] Running command: blastn -query GCF_006974145.1_ASM697414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4693a93-52f5-4eab-ad64-8c16d91a400a/dqc_reference/reference_markers.fasta -out GCF_006974145.1_ASM697414v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:46,481] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:46,485] [INFO] Selected 26 target genomes.
[2024-01-24 12:13:46,486] [INFO] Target genome list was writen to GCF_006974145.1_ASM697414v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:46,494] [INFO] Task started: fastANI
[2024-01-24 12:13:46,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3913057-03dd-46ad-931b-bc8c7ba9c4d8/GCF_006974145.1_ASM697414v1_genomic.fna.gz --refList GCF_006974145.1_ASM697414v1_genomic.fna/target_genomes.txt --output GCF_006974145.1_ASM697414v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:04,622] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:04,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4693a93-52f5-4eab-ad64-8c16d91a400a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:04,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4693a93-52f5-4eab-ad64-8c16d91a400a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:04,642] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:04,642] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:04,642] [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
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	100.0	1375	1376	95	conclusive
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.367	382	1376	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.2578	363	1376	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.2252	366	1376	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	78.1382	272	1376	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	78.0646	311	1376	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.0482	347	1376	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.9536	355	1376	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	77.9478	355	1376	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.9445	354	1376	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	77.8596	262	1376	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.8554	406	1376	95	below_threshold
Snuella sedimenti	strain=CAU 1569	GCA_016428595.1	2798802	2798802	type	True	77.826	260	1376	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.69	247	1376	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	77.6377	295	1376	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.5466	207	1376	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.5138	283	1376	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	77.4126	203	1376	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.3575	212	1376	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.1838	203	1376	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.1713	273	1376	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	77.0289	222	1376	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	76.6363	69	1376	95	below_threshold
Flavobacterium aquicola	strain=DSM 100880	GCA_003385115.1	1682742	1682742	type	True	76.238	60	1376	95	below_threshold
Myroides guanonis	strain=DSM 26542	GCA_900114085.1	1150112	1150112	type	True	75.9262	50	1376	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:04,645] [INFO] DFAST Taxonomy check result was written to GCF_006974145.1_ASM697414v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:04,645] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:04,646] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:04,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4693a93-52f5-4eab-ad64-8c16d91a400a/dqc_reference/checkm_data
[2024-01-24 12:14:04,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:04,693] [INFO] Task started: CheckM
[2024-01-24 12:14:04,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006974145.1_ASM697414v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006974145.1_ASM697414v1_genomic.fna/checkm_input GCF_006974145.1_ASM697414v1_genomic.fna/checkm_result
[2024-01-24 12:14:52,151] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:52,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:52,172] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:52,172] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:52,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006974145.1_ASM697414v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:52,173] [INFO] Task started: Blastn
[2024-01-24 12:14:52,173] [INFO] Running command: blastn -query GCF_006974145.1_ASM697414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4693a93-52f5-4eab-ad64-8c16d91a400a/dqc_reference/reference_markers_gtdb.fasta -out GCF_006974145.1_ASM697414v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:53,196] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:53,201] [INFO] Selected 24 target genomes.
[2024-01-24 12:14:53,201] [INFO] Target genome list was writen to GCF_006974145.1_ASM697414v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:53,227] [INFO] Task started: fastANI
[2024-01-24 12:14:53,227] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3913057-03dd-46ad-931b-bc8c7ba9c4d8/GCF_006974145.1_ASM697414v1_genomic.fna.gz --refList GCF_006974145.1_ASM697414v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006974145.1_ASM697414v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:10,135] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:10,152] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:10,153] [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_006974145.1	s__Changchengzhania lutea	100.0	1376	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Changchengzhania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000789235.1	s__Wocania ichthyoenteri	78.7865	433	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.6677	483	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	78.337	359	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.235	365	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	78.1352	272	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	78.1189	319	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002893765.1	s__Tamlana_A carrageenivorans	78.0859	269	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003425985.1	s__Mariniflexile sp002848895	78.0616	342	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.0241	339	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	78.0165	397	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006148925.1	s__Algibacter_D aestuarii	78.0019	309	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	77.9443	352	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.8504	405	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796805.1	s__Algibacter sp009796805	77.84	335	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498295.1	s__Wocania sp009498295	77.7587	250	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	77.712	248	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002784145.1	s__Yeosuana sp002784145	77.5808	273	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCF_008084905.1	s__Xanthomarina maritima	77.5371	225	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	77.3461	200	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404085.1	s__Winogradskyella helgolandensis	77.2011	200	1376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:10,154] [INFO] GTDB search result was written to GCF_006974145.1_ASM697414v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:10,155] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:10,160] [INFO] DFAST_QC result json was written to GCF_006974145.1_ASM697414v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:10,161] [INFO] DFAST_QC completed!
[2024-01-24 12:15:10,161] [INFO] Total running time: 0h1m41s