[2024-01-25 19:04:50,659] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:50,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:50,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg29ec04e4-ec7c-4407-8f80-7d9ed8eeaf5f/dqc_reference
[2024-01-25 19:04:51,781] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:51,781] [INFO] Task started: Prodigal
[2024-01-25 19:04:51,782] [INFO] Running command: gunzip -c /var/lib/cwl/stg431c407a-4a25-4312-9610-b073017773c3/GCF_009746565.1_ASM974656v1_genomic.fna.gz | prodigal -d GCF_009746565.1_ASM974656v1_genomic.fna/cds.fna -a GCF_009746565.1_ASM974656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:05,547] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:05,547] [INFO] Task started: HMMsearch
[2024-01-25 19:05:05,547] [INFO] Running command: hmmsearch --tblout GCF_009746565.1_ASM974656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29ec04e4-ec7c-4407-8f80-7d9ed8eeaf5f/dqc_reference/reference_markers.hmm GCF_009746565.1_ASM974656v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:05,827] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:05,828] [INFO] Found 6/6 markers.
[2024-01-25 19:05:05,862] [INFO] Query marker FASTA was written to GCF_009746565.1_ASM974656v1_genomic.fna/markers.fasta
[2024-01-25 19:05:05,863] [INFO] Task started: Blastn
[2024-01-25 19:05:05,863] [INFO] Running command: blastn -query GCF_009746565.1_ASM974656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29ec04e4-ec7c-4407-8f80-7d9ed8eeaf5f/dqc_reference/reference_markers.fasta -out GCF_009746565.1_ASM974656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:06,554] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:06,557] [INFO] Selected 19 target genomes.
[2024-01-25 19:05:06,557] [INFO] Target genome list was writen to GCF_009746565.1_ASM974656v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:06,571] [INFO] Task started: fastANI
[2024-01-25 19:05:06,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg431c407a-4a25-4312-9610-b073017773c3/GCF_009746565.1_ASM974656v1_genomic.fna.gz --refList GCF_009746565.1_ASM974656v1_genomic.fna/target_genomes.txt --output GCF_009746565.1_ASM974656v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:18,844] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:18,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29ec04e4-ec7c-4407-8f80-7d9ed8eeaf5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:18,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29ec04e4-ec7c-4407-8f80-7d9ed8eeaf5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:18,855] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:05:18,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:05:18,856] [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
Mariniflexile maritimum	strain=M5A1M	GCA_009746565.1	2682493	2682493	type	True	100.0	1198	1199	95	conclusive
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	79.7955	497	1199	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	79.1548	531	1199	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	78.2376	324	1199	95	below_threshold
Confluentibacter citreus	strain=XJNY	GCA_002807055.1	2007307	2007307	type	True	78.1273	320	1199	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	78.041	320	1199	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.6756	287	1199	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.2328	177	1199	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.2217	143	1199	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	77.1825	92	1199	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.1736	116	1199	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.0153	175	1199	95	below_threshold
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	76.9179	130	1199	95	below_threshold
Mangrovimonas yunxiaonensis	strain=LY01	GCA_000733475.1	1197477	1197477	type	True	76.8952	138	1199	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.8499	152	1199	95	below_threshold
Formosa agariphila	strain=type strain: KMM 3901	GCA_000723205.1	320324	320324	type	True	76.7842	133	1199	95	below_threshold
Aestuariivivens sediminis	strain=S-DT1-15	GCA_022662105.1	2913557	2913557	type	True	76.7147	154	1199	95	below_threshold
Mangrovimonas yunxiaonensis	strain=CGMCC 1.12280	GCA_014636995.1	1197477	1197477	type	True	76.7085	140	1199	95	below_threshold
Formosa algae	strain=KMM 3553	GCA_001439665.1	225843	225843	type	True	76.5632	144	1199	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:18,857] [INFO] DFAST Taxonomy check result was written to GCF_009746565.1_ASM974656v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:18,858] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:18,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:18,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29ec04e4-ec7c-4407-8f80-7d9ed8eeaf5f/dqc_reference/checkm_data
[2024-01-25 19:05:18,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:18,898] [INFO] Task started: CheckM
[2024-01-25 19:05:18,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009746565.1_ASM974656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009746565.1_ASM974656v1_genomic.fna/checkm_input GCF_009746565.1_ASM974656v1_genomic.fna/checkm_result
[2024-01-25 19:05:58,203] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:58,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:58,221] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:58,222] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:58,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009746565.1_ASM974656v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:58,222] [INFO] Task started: Blastn
[2024-01-25 19:05:58,222] [INFO] Running command: blastn -query GCF_009746565.1_ASM974656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29ec04e4-ec7c-4407-8f80-7d9ed8eeaf5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009746565.1_ASM974656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:59,050] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:59,054] [INFO] Selected 17 target genomes.
[2024-01-25 19:05:59,054] [INFO] Target genome list was writen to GCF_009746565.1_ASM974656v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:59,079] [INFO] Task started: fastANI
[2024-01-25 19:05:59,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg431c407a-4a25-4312-9610-b073017773c3/GCF_009746565.1_ASM974656v1_genomic.fna.gz --refList GCF_009746565.1_ASM974656v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009746565.1_ASM974656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:11,427] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:11,438] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:06:11,438] [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_009746565.1	s__Mariniflexile sp002426835	100.0	1198	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	98.94	98.94	0.97	0.97	2	conclusive
GCF_017814435.1	s__Mariniflexile gromovii	79.7947	497	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	79.1456	532	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003425985.1	s__Mariniflexile sp002848895	79.0788	541	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002806995.1	s__Confluentibacter lentus	78.2376	324	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807055.1	s__Confluentibacter citreus	78.1319	321	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	78.0759	328	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	77.6885	278	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280395.1	s__Confluentibacter sp002280395	77.6817	211	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258355.1	s__Confluentibacter sp003258355	77.6762	287	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426015.1	s__Aquaticitalea sp002426015	77.5063	166	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348685.1	s__Xanthomarina gelatinilytica	77.2328	177	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	98.37	98.31	0.90	0.88	4	-
GCF_009796805.1	s__Algibacter sp009796805	77.2019	248	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249045.1	s__Winogradskyella eckloniae	77.1834	91	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197735.1	s__Formosa sediminum	76.9352	130	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733475.1	s__Mangrovimonas yunxiaonensis	76.8619	139	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	98.99	97.98	0.98	0.97	3	-
GCF_004115975.1	s__Gelidibacter gilvus	76.3127	133	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:06:11,439] [INFO] GTDB search result was written to GCF_009746565.1_ASM974656v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:11,440] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:11,445] [INFO] DFAST_QC result json was written to GCF_009746565.1_ASM974656v1_genomic.fna/dqc_result.json
[2024-01-25 19:06:11,446] [INFO] DFAST_QC completed!
[2024-01-25 19:06:11,446] [INFO] Total running time: 0h1m21s