[2024-01-24 12:22:33,731] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:33,735] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:33,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg46a7c9eb-e1f0-4acf-8319-6d4b0fb1679e/dqc_reference
[2024-01-24 12:22:35,013] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,014] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,014] [INFO] Running command: gunzip -c /var/lib/cwl/stgfce3cb71-0711-42e3-8626-afb74ae46a1a/GCF_014270105.1_ASM1427010v1_genomic.fna.gz | prodigal -d GCF_014270105.1_ASM1427010v1_genomic.fna/cds.fna -a GCF_014270105.1_ASM1427010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:54,057] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:54,057] [INFO] Task started: HMMsearch
[2024-01-24 12:22:54,057] [INFO] Running command: hmmsearch --tblout GCF_014270105.1_ASM1427010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46a7c9eb-e1f0-4acf-8319-6d4b0fb1679e/dqc_reference/reference_markers.hmm GCF_014270105.1_ASM1427010v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:54,344] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:54,345] [INFO] Found 6/6 markers.
[2024-01-24 12:22:54,390] [INFO] Query marker FASTA was written to GCF_014270105.1_ASM1427010v1_genomic.fna/markers.fasta
[2024-01-24 12:22:54,390] [INFO] Task started: Blastn
[2024-01-24 12:22:54,391] [INFO] Running command: blastn -query GCF_014270105.1_ASM1427010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46a7c9eb-e1f0-4acf-8319-6d4b0fb1679e/dqc_reference/reference_markers.fasta -out GCF_014270105.1_ASM1427010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:55,089] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:55,094] [INFO] Selected 19 target genomes.
[2024-01-24 12:22:55,094] [INFO] Target genome list was writen to GCF_014270105.1_ASM1427010v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:55,100] [INFO] Task started: fastANI
[2024-01-24 12:22:55,100] [INFO] Running command: fastANI --query /var/lib/cwl/stgfce3cb71-0711-42e3-8626-afb74ae46a1a/GCF_014270105.1_ASM1427010v1_genomic.fna.gz --refList GCF_014270105.1_ASM1427010v1_genomic.fna/target_genomes.txt --output GCF_014270105.1_ASM1427010v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:09,084] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:09,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46a7c9eb-e1f0-4acf-8319-6d4b0fb1679e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:09,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46a7c9eb-e1f0-4acf-8319-6d4b0fb1679e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:09,104] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:09,104] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:09,104] [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
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	100.0	1300	1300	95	conclusive
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	78.9949	410	1300	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	78.8331	385	1300	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	78.3489	392	1300	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	78.2873	391	1300	95	below_threshold
Tamlana crocina	strain=HST1-43	GCA_012037625.1	393006	393006	type	True	77.8796	299	1300	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	77.7092	235	1300	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.4786	193	1300	95	below_threshold
Snuella sedimenti	strain=CAU 1569	GCA_016428595.1	2798802	2798802	type	True	77.3941	161	1300	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.3716	183	1300	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.3669	240	1300	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.3438	175	1300	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.3049	255	1300	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.2916	255	1300	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.1331	192	1300	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.8546	114	1300	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.7502	114	1300	95	below_threshold
Aestuariivivens sediminis	strain=S-DT1-15	GCA_022662105.1	2913557	2913557	type	True	76.6979	154	1300	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	76.3695	57	1300	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:09,106] [INFO] DFAST Taxonomy check result was written to GCF_014270105.1_ASM1427010v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:09,107] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:09,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:09,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46a7c9eb-e1f0-4acf-8319-6d4b0fb1679e/dqc_reference/checkm_data
[2024-01-24 12:23:09,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:09,156] [INFO] Task started: CheckM
[2024-01-24 12:23:09,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014270105.1_ASM1427010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014270105.1_ASM1427010v1_genomic.fna/checkm_input GCF_014270105.1_ASM1427010v1_genomic.fna/checkm_result
[2024-01-24 12:24:01,810] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:01,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:01,837] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:01,837] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:01,837] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014270105.1_ASM1427010v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:01,838] [INFO] Task started: Blastn
[2024-01-24 12:24:01,838] [INFO] Running command: blastn -query GCF_014270105.1_ASM1427010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46a7c9eb-e1f0-4acf-8319-6d4b0fb1679e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014270105.1_ASM1427010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:02,714] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:02,718] [INFO] Selected 18 target genomes.
[2024-01-24 12:24:02,718] [INFO] Target genome list was writen to GCF_014270105.1_ASM1427010v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:02,732] [INFO] Task started: fastANI
[2024-01-24 12:24:02,732] [INFO] Running command: fastANI --query /var/lib/cwl/stgfce3cb71-0711-42e3-8626-afb74ae46a1a/GCF_014270105.1_ASM1427010v1_genomic.fna.gz --refList GCF_014270105.1_ASM1427010v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014270105.1_ASM1427010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:15,207] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:15,225] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:15,225] [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_014270105.1	s__Jejuia sp014270105	100.0	1300	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004310325.1	s__Jejuia sp004310325	78.996	411	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016827605.1	s__Jejuia sp016827605	78.8466	385	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310335.1	s__Jejuia pacifica	78.3585	391	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900111025.1	s__Jejuia jejuensis	78.2995	370	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428965.1	s__Jejuia sp002428965	78.2896	340	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973595.1	s__Jejuia pallidilutea	78.0565	341	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	98.03	97.97	0.83	0.83	4	-
GCF_004358095.2	s__Seonamhaeicola sp004358095	78.0519	290	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	77.6056	211	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910715.1	s__Flavivirga sp012910715	77.4783	193	1300	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	77.4027	212	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.3716	183	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883545.1	s__Confluentibacter sp018883545	77.3142	188	1300	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	77.3058	253	1300	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_007997385.1	s__Seonamhaeicola algicola	77.263	208	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	77.2623	207	1300	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	77.1961	185	1300	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_000941055.1	s__Siansivirga zeaxanthinifaciens	77.0691	188	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:15,227] [INFO] GTDB search result was written to GCF_014270105.1_ASM1427010v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:15,229] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:15,233] [INFO] DFAST_QC result json was written to GCF_014270105.1_ASM1427010v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:15,233] [INFO] DFAST_QC completed!
[2024-01-24 12:24:15,233] [INFO] Total running time: 0h1m42s