[2024-01-24 11:26:11,414] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:11,417] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:11,417] [INFO] DQC Reference Directory: /var/lib/cwl/stga8e8fff0-162d-46da-b441-2c7eb5fc9937/dqc_reference
[2024-01-24 11:26:12,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:12,809] [INFO] Task started: Prodigal
[2024-01-24 11:26:12,809] [INFO] Running command: gunzip -c /var/lib/cwl/stg75657c74-62b3-4e74-a3cd-62e10efae6da/GCF_014646655.1_ASM1464665v1_genomic.fna.gz | prodigal -d GCF_014646655.1_ASM1464665v1_genomic.fna/cds.fna -a GCF_014646655.1_ASM1464665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:29,448] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:29,448] [INFO] Task started: HMMsearch
[2024-01-24 11:26:29,448] [INFO] Running command: hmmsearch --tblout GCF_014646655.1_ASM1464665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8e8fff0-162d-46da-b441-2c7eb5fc9937/dqc_reference/reference_markers.hmm GCF_014646655.1_ASM1464665v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:29,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:29,768] [INFO] Found 6/6 markers.
[2024-01-24 11:26:29,800] [INFO] Query marker FASTA was written to GCF_014646655.1_ASM1464665v1_genomic.fna/markers.fasta
[2024-01-24 11:26:29,800] [INFO] Task started: Blastn
[2024-01-24 11:26:29,800] [INFO] Running command: blastn -query GCF_014646655.1_ASM1464665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8e8fff0-162d-46da-b441-2c7eb5fc9937/dqc_reference/reference_markers.fasta -out GCF_014646655.1_ASM1464665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:30,486] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:30,490] [INFO] Selected 23 target genomes.
[2024-01-24 11:26:30,490] [INFO] Target genome list was writen to GCF_014646655.1_ASM1464665v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:30,497] [INFO] Task started: fastANI
[2024-01-24 11:26:30,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg75657c74-62b3-4e74-a3cd-62e10efae6da/GCF_014646655.1_ASM1464665v1_genomic.fna.gz --refList GCF_014646655.1_ASM1464665v1_genomic.fna/target_genomes.txt --output GCF_014646655.1_ASM1464665v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:49,387] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:49,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8e8fff0-162d-46da-b441-2c7eb5fc9937/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:49,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8e8fff0-162d-46da-b441-2c7eb5fc9937/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:49,409] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:49,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:49,410] [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
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	100.0	1239	1239	95	conclusive
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	80.1921	638	1239	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	78.1046	350	1239	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.967	328	1239	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	77.8755	335	1239	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	77.8549	351	1239	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	77.7813	366	1239	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.6801	279	1239	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.632	279	1239	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.6029	292	1239	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.5603	211	1239	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	77.5207	279	1239	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.4643	196	1239	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	77.4641	206	1239	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.4354	269	1239	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.3924	259	1239	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	77.3821	267	1239	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.2955	208	1239	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	77.1812	227	1239	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.1649	191	1239	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.0217	208	1239	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.9494	208	1239	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	76.7416	178	1239	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:49,412] [INFO] DFAST Taxonomy check result was written to GCF_014646655.1_ASM1464665v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:49,412] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:49,412] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:49,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8e8fff0-162d-46da-b441-2c7eb5fc9937/dqc_reference/checkm_data
[2024-01-24 11:26:49,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:49,453] [INFO] Task started: CheckM
[2024-01-24 11:26:49,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646655.1_ASM1464665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646655.1_ASM1464665v1_genomic.fna/checkm_input GCF_014646655.1_ASM1464665v1_genomic.fna/checkm_result
[2024-01-24 11:27:37,350] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:37,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:37,374] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:37,375] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:37,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646655.1_ASM1464665v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:37,376] [INFO] Task started: Blastn
[2024-01-24 11:27:37,376] [INFO] Running command: blastn -query GCF_014646655.1_ASM1464665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8e8fff0-162d-46da-b441-2c7eb5fc9937/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646655.1_ASM1464665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:38,279] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:38,284] [INFO] Selected 20 target genomes.
[2024-01-24 11:27:38,284] [INFO] Target genome list was writen to GCF_014646655.1_ASM1464665v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:38,313] [INFO] Task started: fastANI
[2024-01-24 11:27:38,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg75657c74-62b3-4e74-a3cd-62e10efae6da/GCF_014646655.1_ASM1464665v1_genomic.fna.gz --refList GCF_014646655.1_ASM1464665v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646655.1_ASM1464665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:51,755] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:51,779] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:51,780] [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_014646655.1	s__Yeosuana aromativorans	100.0	1239	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011762485.1	s__Yeosuana marina	80.1832	638	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441545.1	s__Yeosuana sp002441545	79.1602	475	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002784145.1	s__Yeosuana sp002784145	78.7055	462	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCA_003258355.1	s__Confluentibacter sp003258355	77.9776	327	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	77.8555	351	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	77.7661	319	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883545.1	s__Confluentibacter sp018883545	77.7428	280	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	77.6702	279	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003425985.1	s__Mariniflexile sp002848895	77.6447	385	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.6434	278	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	77.5531	287	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	77.4994	280	1239	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_012931685.1	s__Pseudobizionia ponticola	77.4823	206	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudobizionia	95.0	97.35	97.35	0.92	0.92	2	-
GCF_002895005.1	s__Hanstruepera neustonica	77.4643	196	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hanstruepera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148645.1	s__Xanthomarina spongicola	77.4612	201	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	77.4199	286	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428965.1	s__Jejuia sp002428965	77.1979	178	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	77.1385	241	1239	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_000425305.1	s__Psychroserpens burtonensis	76.513	143	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:51,782] [INFO] GTDB search result was written to GCF_014646655.1_ASM1464665v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:51,783] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:51,788] [INFO] DFAST_QC result json was written to GCF_014646655.1_ASM1464665v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:51,788] [INFO] DFAST_QC completed!
[2024-01-24 11:27:51,788] [INFO] Total running time: 0h1m40s