[2024-01-24 13:22:40,622] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:40,624] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:40,624] [INFO] DQC Reference Directory: /var/lib/cwl/stg123575bb-ec23-4d74-863a-e5f120c3840e/dqc_reference
[2024-01-24 13:22:41,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:41,833] [INFO] Task started: Prodigal
[2024-01-24 13:22:41,833] [INFO] Running command: gunzip -c /var/lib/cwl/stg7961d2dd-b2f8-4142-9ca9-d6de64ee2b84/GCF_017814435.1_ASM1781443v1_genomic.fna.gz | prodigal -d GCF_017814435.1_ASM1781443v1_genomic.fna/cds.fna -a GCF_017814435.1_ASM1781443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:57,764] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:57,765] [INFO] Task started: HMMsearch
[2024-01-24 13:22:57,765] [INFO] Running command: hmmsearch --tblout GCF_017814435.1_ASM1781443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg123575bb-ec23-4d74-863a-e5f120c3840e/dqc_reference/reference_markers.hmm GCF_017814435.1_ASM1781443v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:58,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:58,053] [INFO] Found 6/6 markers.
[2024-01-24 13:22:58,091] [INFO] Query marker FASTA was written to GCF_017814435.1_ASM1781443v1_genomic.fna/markers.fasta
[2024-01-24 13:22:58,092] [INFO] Task started: Blastn
[2024-01-24 13:22:58,092] [INFO] Running command: blastn -query GCF_017814435.1_ASM1781443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg123575bb-ec23-4d74-863a-e5f120c3840e/dqc_reference/reference_markers.fasta -out GCF_017814435.1_ASM1781443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:58,819] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:58,822] [INFO] Selected 19 target genomes.
[2024-01-24 13:22:58,823] [INFO] Target genome list was writen to GCF_017814435.1_ASM1781443v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:58,842] [INFO] Task started: fastANI
[2024-01-24 13:22:58,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg7961d2dd-b2f8-4142-9ca9-d6de64ee2b84/GCF_017814435.1_ASM1781443v1_genomic.fna.gz --refList GCF_017814435.1_ASM1781443v1_genomic.fna/target_genomes.txt --output GCF_017814435.1_ASM1781443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:14,428] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:14,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg123575bb-ec23-4d74-863a-e5f120c3840e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:14,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg123575bb-ec23-4d74-863a-e5f120c3840e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:14,444] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:14,444] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:14,445] [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
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	100.0	1399	1399	95	conclusive
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	83.6298	914	1399	95	below_threshold
Mariniflexile maritimum	strain=M5A1M	GCA_009746565.1	2682493	2682493	type	True	79.5279	512	1399	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	78.7128	453	1399	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	78.7006	477	1399	95	below_threshold
Confluentibacter citreus	strain=XJNY	GCA_002807055.1	2007307	2007307	type	True	78.6453	446	1399	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.6015	475	1399	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.6003	478	1399	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.5964	475	1399	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.4291	415	1399	95	below_threshold
Aestuariibaculum suncheonense	strain=SC17	GCA_014596935.1	1028745	1028745	type	True	78.4204	411	1399	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.3963	387	1399	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.3847	409	1399	95	below_threshold
Aestuariibaculum marinum	strain=IP7	GCA_014596975.1	2683592	2683592	type	True	78.3627	389	1399	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	78.3447	409	1399	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	78.0957	403	1399	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.7055	307	1399	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.5401	273	1399	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.3689	298	1399	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:14,446] [INFO] DFAST Taxonomy check result was written to GCF_017814435.1_ASM1781443v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:14,447] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:14,447] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:14,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg123575bb-ec23-4d74-863a-e5f120c3840e/dqc_reference/checkm_data
[2024-01-24 13:23:14,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:14,497] [INFO] Task started: CheckM
[2024-01-24 13:23:14,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017814435.1_ASM1781443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017814435.1_ASM1781443v1_genomic.fna/checkm_input GCF_017814435.1_ASM1781443v1_genomic.fna/checkm_result
[2024-01-24 13:24:00,514] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:00,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:00,536] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:00,536] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:00,537] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017814435.1_ASM1781443v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:00,537] [INFO] Task started: Blastn
[2024-01-24 13:24:00,537] [INFO] Running command: blastn -query GCF_017814435.1_ASM1781443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg123575bb-ec23-4d74-863a-e5f120c3840e/dqc_reference/reference_markers_gtdb.fasta -out GCF_017814435.1_ASM1781443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:01,524] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:01,529] [INFO] Selected 14 target genomes.
[2024-01-24 13:24:01,529] [INFO] Target genome list was writen to GCF_017814435.1_ASM1781443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:01,569] [INFO] Task started: fastANI
[2024-01-24 13:24:01,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg7961d2dd-b2f8-4142-9ca9-d6de64ee2b84/GCF_017814435.1_ASM1781443v1_genomic.fna.gz --refList GCF_017814435.1_ASM1781443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017814435.1_ASM1781443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:12,278] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:12,295] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:12,295] [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_017814435.1	s__Mariniflexile gromovii	100.0	1399	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004341235.1	s__Mariniflexile fucanivorans	83.6351	913	1399	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	82.1864	764	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	79.5448	473	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009746565.1	s__Mariniflexile sp002426835	79.5257	513	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	98.94	98.94	0.97	0.97	2	-
GCF_900114265.1	s__Flaviramulus basaltis	78.9895	518	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280395.1	s__Confluentibacter sp002280395	78.8334	267	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	78.746	487	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843175.1	s__Confluentibacter flavum	78.7206	487	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806995.1	s__Confluentibacter lentus	78.7128	453	1399	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	78.6855	478	1399	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	78.6546	445	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	78.6054	479	1399	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_014596975.1	s__Aestuariibaculum marinum	78.3526	390	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:12,297] [INFO] GTDB search result was written to GCF_017814435.1_ASM1781443v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:12,298] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:12,302] [INFO] DFAST_QC result json was written to GCF_017814435.1_ASM1781443v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:12,303] [INFO] DFAST_QC completed!
[2024-01-24 13:24:12,303] [INFO] Total running time: 0h1m32s