[2024-01-24 11:12:56,318] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:56,320] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:56,321] [INFO] DQC Reference Directory: /var/lib/cwl/stgf18e5772-2134-4052-bd22-f5a0567d6f46/dqc_reference
[2024-01-24 11:12:57,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:57,687] [INFO] Task started: Prodigal
[2024-01-24 11:12:57,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg19c97cf1-8e0b-45d8-98e8-56a6b4c6b67e/GCF_008085455.1_ASM808545v1_genomic.fna.gz | prodigal -d GCF_008085455.1_ASM808545v1_genomic.fna/cds.fna -a GCF_008085455.1_ASM808545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:12,809] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:12,809] [INFO] Task started: HMMsearch
[2024-01-24 11:13:12,810] [INFO] Running command: hmmsearch --tblout GCF_008085455.1_ASM808545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf18e5772-2134-4052-bd22-f5a0567d6f46/dqc_reference/reference_markers.hmm GCF_008085455.1_ASM808545v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:13,181] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:13,182] [INFO] Found 6/6 markers.
[2024-01-24 11:13:13,224] [INFO] Query marker FASTA was written to GCF_008085455.1_ASM808545v1_genomic.fna/markers.fasta
[2024-01-24 11:13:13,225] [INFO] Task started: Blastn
[2024-01-24 11:13:13,225] [INFO] Running command: blastn -query GCF_008085455.1_ASM808545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf18e5772-2134-4052-bd22-f5a0567d6f46/dqc_reference/reference_markers.fasta -out GCF_008085455.1_ASM808545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:13,897] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:13,900] [INFO] Selected 17 target genomes.
[2024-01-24 11:13:13,900] [INFO] Target genome list was writen to GCF_008085455.1_ASM808545v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:13,905] [INFO] Task started: fastANI
[2024-01-24 11:13:13,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg19c97cf1-8e0b-45d8-98e8-56a6b4c6b67e/GCF_008085455.1_ASM808545v1_genomic.fna.gz --refList GCF_008085455.1_ASM808545v1_genomic.fna/target_genomes.txt --output GCF_008085455.1_ASM808545v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:27,383] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:27,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf18e5772-2134-4052-bd22-f5a0567d6f46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:27,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf18e5772-2134-4052-bd22-f5a0567d6f46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:27,400] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:27,401] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:27,401] [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
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	99.9993	1520	1523	95	conclusive
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	80.0225	656	1523	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	78.8233	574	1523	95	below_threshold
Seonamhaeicola aphaedonensis	strain=CECT 8487	GCA_003386195.1	1461338	1461338	type	True	78.5669	434	1523	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.9703	350	1523	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.9526	354	1523	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	77.8564	296	1523	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.6972	356	1523	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.691	402	1523	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.6066	179	1523	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.4996	303	1523	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	77.4556	330	1523	95	below_threshold
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	77.3191	198	1523	95	below_threshold
Snuella sedimenti	strain=CAU 1569	GCA_016428595.1	2798802	2798802	type	True	77.215	242	1523	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	77.0149	216	1523	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.9746	186	1523	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	75.8227	76	1523	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:27,403] [INFO] DFAST Taxonomy check result was written to GCF_008085455.1_ASM808545v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:27,403] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:27,404] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:27,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf18e5772-2134-4052-bd22-f5a0567d6f46/dqc_reference/checkm_data
[2024-01-24 11:13:27,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:27,453] [INFO] Task started: CheckM
[2024-01-24 11:13:27,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008085455.1_ASM808545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008085455.1_ASM808545v1_genomic.fna/checkm_input GCF_008085455.1_ASM808545v1_genomic.fna/checkm_result
[2024-01-24 11:14:14,816] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:14,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 34.07%
Strain heterogeneity: 96.55%
--------------------------------------------------------------------------------
[2024-01-24 11:14:14,841] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:14,841] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:14,842] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008085455.1_ASM808545v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:14,842] [INFO] Task started: Blastn
[2024-01-24 11:14:14,842] [INFO] Running command: blastn -query GCF_008085455.1_ASM808545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf18e5772-2134-4052-bd22-f5a0567d6f46/dqc_reference/reference_markers_gtdb.fasta -out GCF_008085455.1_ASM808545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:15,813] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:15,817] [INFO] Selected 18 target genomes.
[2024-01-24 11:14:15,818] [INFO] Target genome list was writen to GCF_008085455.1_ASM808545v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:15,831] [INFO] Task started: fastANI
[2024-01-24 11:14:15,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg19c97cf1-8e0b-45d8-98e8-56a6b4c6b67e/GCF_008085455.1_ASM808545v1_genomic.fna.gz --refList GCF_008085455.1_ASM808545v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008085455.1_ASM808545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:29,343] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:29,364] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:14:29,365] [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_007997385.1	s__Seonamhaeicola algicola	80.0225	656	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	79.2967	499	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	78.812	577	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358095.2	s__Seonamhaeicola sp004358095	78.7653	431	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386195.1	s__Seonamhaeicola aphaedonensis	78.5719	434	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.2261	377	1523	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_900114265.1	s__Flaviramulus basaltis	78.0582	400	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	77.9578	352	1523	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_002973595.1	s__Jejuia pallidilutea	77.8018	322	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	98.03	97.97	0.83	0.83	4	-
GCF_016827605.1	s__Jejuia sp016827605	77.7057	355	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	77.6976	312	1523	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_004791695.1	s__Flavivirga rizhaonensis	77.6973	402	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814435.1	s__Mariniflexile gromovii	77.6859	297	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428965.1	s__Jejuia sp002428965	77.6703	386	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003425985.1	s__Mariniflexile sp002848895	77.555	291	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004310325.1	s__Jejuia sp004310325	77.5229	300	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	77.4511	332	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428595.1	s__Snuella sp016428595	77.2037	243	1523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Snuella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:29,366] [INFO] GTDB search result was written to GCF_008085455.1_ASM808545v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:29,367] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:29,370] [INFO] DFAST_QC result json was written to GCF_008085455.1_ASM808545v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:29,370] [INFO] DFAST_QC completed!
[2024-01-24 11:14:29,371] [INFO] Total running time: 0h1m33s