[2024-01-24 14:42:14,442] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:42:14,444] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:42:14,444] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e438e54-600d-4cd0-888d-756376a8133d/dqc_reference
[2024-01-24 14:42:15,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:42:15,742] [INFO] Task started: Prodigal
[2024-01-24 14:42:15,742] [INFO] Running command: gunzip -c /var/lib/cwl/stgd651f2cf-d1ca-474d-9ffd-77523eb723a6/GCF_002886045.1_ASM288604v1_genomic.fna.gz | prodigal -d GCF_002886045.1_ASM288604v1_genomic.fna/cds.fna -a GCF_002886045.1_ASM288604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:42:34,768] [INFO] Task succeeded: Prodigal
[2024-01-24 14:42:34,768] [INFO] Task started: HMMsearch
[2024-01-24 14:42:34,769] [INFO] Running command: hmmsearch --tblout GCF_002886045.1_ASM288604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e438e54-600d-4cd0-888d-756376a8133d/dqc_reference/reference_markers.hmm GCF_002886045.1_ASM288604v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:42:35,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:42:35,103] [INFO] Found 6/6 markers.
[2024-01-24 14:42:35,153] [INFO] Query marker FASTA was written to GCF_002886045.1_ASM288604v1_genomic.fna/markers.fasta
[2024-01-24 14:42:35,153] [INFO] Task started: Blastn
[2024-01-24 14:42:35,154] [INFO] Running command: blastn -query GCF_002886045.1_ASM288604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e438e54-600d-4cd0-888d-756376a8133d/dqc_reference/reference_markers.fasta -out GCF_002886045.1_ASM288604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:35,886] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:35,890] [INFO] Selected 19 target genomes.
[2024-01-24 14:42:35,891] [INFO] Target genome list was writen to GCF_002886045.1_ASM288604v1_genomic.fna/target_genomes.txt
[2024-01-24 14:42:35,900] [INFO] Task started: fastANI
[2024-01-24 14:42:35,900] [INFO] Running command: fastANI --query /var/lib/cwl/stgd651f2cf-d1ca-474d-9ffd-77523eb723a6/GCF_002886045.1_ASM288604v1_genomic.fna.gz --refList GCF_002886045.1_ASM288604v1_genomic.fna/target_genomes.txt --output GCF_002886045.1_ASM288604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:42:51,418] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:51,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e438e54-600d-4cd0-888d-756376a8133d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:42:51,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e438e54-600d-4cd0-888d-756376a8133d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:42:51,445] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:42:51,445] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:42:51,445] [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
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	100.0	1887	1888	95	conclusive
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	81.3114	869	1888	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	80.4965	844	1888	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.5333	388	1888	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.4542	411	1888	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.393	445	1888	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.2762	391	1888	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.2586	392	1888	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	78.1841	292	1888	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	78.1602	404	1888	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.103	405	1888	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	77.981	326	1888	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.916	347	1888	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.7653	302	1888	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.6718	217	1888	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.6386	274	1888	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.589	383	1888	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.5857	282	1888	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	77.5073	327	1888	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:42:51,447] [INFO] DFAST Taxonomy check result was written to GCF_002886045.1_ASM288604v1_genomic.fna/tc_result.tsv
[2024-01-24 14:42:51,448] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:42:51,448] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:42:51,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e438e54-600d-4cd0-888d-756376a8133d/dqc_reference/checkm_data
[2024-01-24 14:42:51,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:42:51,506] [INFO] Task started: CheckM
[2024-01-24 14:42:51,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002886045.1_ASM288604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002886045.1_ASM288604v1_genomic.fna/checkm_input GCF_002886045.1_ASM288604v1_genomic.fna/checkm_result
[2024-01-24 14:43:42,821] [INFO] Task succeeded: CheckM
[2024-01-24 14:43:42,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:43:42,843] [INFO] ===== Completeness check finished =====
[2024-01-24 14:43:42,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:43:42,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002886045.1_ASM288604v1_genomic.fna/markers.fasta)
[2024-01-24 14:43:42,844] [INFO] Task started: Blastn
[2024-01-24 14:43:42,844] [INFO] Running command: blastn -query GCF_002886045.1_ASM288604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e438e54-600d-4cd0-888d-756376a8133d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002886045.1_ASM288604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:43:43,799] [INFO] Task succeeded: Blastn
[2024-01-24 14:43:43,803] [INFO] Selected 13 target genomes.
[2024-01-24 14:43:43,804] [INFO] Target genome list was writen to GCF_002886045.1_ASM288604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:43:43,827] [INFO] Task started: fastANI
[2024-01-24 14:43:43,827] [INFO] Running command: fastANI --query /var/lib/cwl/stgd651f2cf-d1ca-474d-9ffd-77523eb723a6/GCF_002886045.1_ASM288604v1_genomic.fna.gz --refList GCF_002886045.1_ASM288604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002886045.1_ASM288604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:43:55,939] [INFO] Task succeeded: fastANI
[2024-01-24 14:43:55,956] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:43:55,956] [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_002886045.1	s__Flavivirga eckloniae	100.0	1888	1888	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004791695.1	s__Flavivirga rizhaonensis	81.3132	869	1888	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910715.1	s__Flavivirga sp012910715	80.4895	845	1888	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.8642	481	1888	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	78.8348	521	1888	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_000789235.1	s__Wocania ichthyoenteri	78.6459	472	1888	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	78.384	445	1888	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_009796805.1	s__Algibacter sp009796805	78.1631	376	1888	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	78.1601	404	1888	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.1087	405	1888	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002893765.1	s__Tamlana_A carrageenivorans	78.0212	326	1888	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_018860245.1	s__Tamlana_A agarivorans_A	78.008	334	1888	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_001310225.1	s__Algibacter_A alginicilyticus	77.9457	350	1888	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:43:55,959] [INFO] GTDB search result was written to GCF_002886045.1_ASM288604v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:43:55,960] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:43:55,964] [INFO] DFAST_QC result json was written to GCF_002886045.1_ASM288604v1_genomic.fna/dqc_result.json
[2024-01-24 14:43:55,964] [INFO] DFAST_QC completed!
[2024-01-24 14:43:55,964] [INFO] Total running time: 0h1m42s