[2024-01-24 13:24:11,885] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:11,886] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:11,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg81bb8f72-e398-4b41-926f-7292b3aa3f82/dqc_reference
[2024-01-24 13:24:13,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:13,152] [INFO] Task started: Prodigal
[2024-01-24 13:24:13,152] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa381d09-db29-4a60-9464-8c935af164a3/GCF_004804315.1_ASM480431v1_genomic.fna.gz | prodigal -d GCF_004804315.1_ASM480431v1_genomic.fna/cds.fna -a GCF_004804315.1_ASM480431v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:33,161] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:33,161] [INFO] Task started: HMMsearch
[2024-01-24 13:24:33,162] [INFO] Running command: hmmsearch --tblout GCF_004804315.1_ASM480431v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81bb8f72-e398-4b41-926f-7292b3aa3f82/dqc_reference/reference_markers.hmm GCF_004804315.1_ASM480431v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:33,389] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:33,390] [INFO] Found 6/6 markers.
[2024-01-24 13:24:33,425] [INFO] Query marker FASTA was written to GCF_004804315.1_ASM480431v1_genomic.fna/markers.fasta
[2024-01-24 13:24:33,426] [INFO] Task started: Blastn
[2024-01-24 13:24:33,426] [INFO] Running command: blastn -query GCF_004804315.1_ASM480431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81bb8f72-e398-4b41-926f-7292b3aa3f82/dqc_reference/reference_markers.fasta -out GCF_004804315.1_ASM480431v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:34,035] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:34,039] [INFO] Selected 18 target genomes.
[2024-01-24 13:24:34,039] [INFO] Target genome list was writen to GCF_004804315.1_ASM480431v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:34,052] [INFO] Task started: fastANI
[2024-01-24 13:24:34,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa381d09-db29-4a60-9464-8c935af164a3/GCF_004804315.1_ASM480431v1_genomic.fna.gz --refList GCF_004804315.1_ASM480431v1_genomic.fna/target_genomes.txt --output GCF_004804315.1_ASM480431v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:45,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:45,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81bb8f72-e398-4b41-926f-7292b3aa3f82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:45,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81bb8f72-e398-4b41-926f-7292b3aa3f82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:45,927] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:24:45,927] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:24:45,927] [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
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	100.0	1377	1378	95	conclusive
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	79.4097	542	1378	95	below_threshold
Muricauda algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	78.3625	375	1378	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	78.2526	355	1378	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	78.1214	340	1378	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	78.0246	256	1378	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	78.003	317	1378	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	77.97	259	1378	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	77.8626	246	1378	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	77.8565	257	1378	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	77.841	250	1378	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	77.6833	253	1378	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	77.4903	251	1378	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.8011	53	1378	95	below_threshold
Arenibacter latericius	strain=DSM 15913	GCA_000424985.1	86104	86104	type	True	76.5416	67	1378	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	76.5277	52	1378	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.3056	83	1378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:24:45,929] [INFO] DFAST Taxonomy check result was written to GCF_004804315.1_ASM480431v1_genomic.fna/tc_result.tsv
[2024-01-24 13:24:45,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:45,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:45,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81bb8f72-e398-4b41-926f-7292b3aa3f82/dqc_reference/checkm_data
[2024-01-24 13:24:45,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:45,972] [INFO] Task started: CheckM
[2024-01-24 13:24:45,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004804315.1_ASM480431v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004804315.1_ASM480431v1_genomic.fna/checkm_input GCF_004804315.1_ASM480431v1_genomic.fna/checkm_result
[2024-01-24 13:25:42,246] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:42,247] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:42,265] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:42,265] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:42,265] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004804315.1_ASM480431v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:42,266] [INFO] Task started: Blastn
[2024-01-24 13:25:42,266] [INFO] Running command: blastn -query GCF_004804315.1_ASM480431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81bb8f72-e398-4b41-926f-7292b3aa3f82/dqc_reference/reference_markers_gtdb.fasta -out GCF_004804315.1_ASM480431v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:43,129] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:43,132] [INFO] Selected 18 target genomes.
[2024-01-24 13:25:43,132] [INFO] Target genome list was writen to GCF_004804315.1_ASM480431v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:43,141] [INFO] Task started: fastANI
[2024-01-24 13:25:43,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa381d09-db29-4a60-9464-8c935af164a3/GCF_004804315.1_ASM480431v1_genomic.fna.gz --refList GCF_004804315.1_ASM480431v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004804315.1_ASM480431v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:55,692] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:55,706] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:55,707] [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_004804315.1	s__Muricauda sp004804315	100.0	1377	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014698935.1	s__Muricauda sp014698935	79.9475	629	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215465.1	s__Muricauda pacifica_A	79.4004	543	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005937185.1	s__Muricauda algicola	78.3831	373	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129665.1	s__Muricauda flava	78.2737	353	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	78.2137	398	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	78.1324	339	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149745.1	s__Muricauda koreensis	78.0631	375	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382275.1	s__Muricauda nanhaiensis	78.0142	316	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102925.1	s__Muricauda zhangzhouensis	77.9838	258	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001683915.1	s__Muricauda sp001683915	77.9636	294	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCA_002699205.1	s__Muricauda sp002699205	77.9148	232	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.91	99.91	0.89	0.89	2	-
GCF_018449435.1	s__Muricauda sp018449435	77.8988	283	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468565.1	s__Muricauda sp010468565	77.8804	246	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581615.1	s__Muricauda lutimaris	77.8752	245	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224085.1	s__Muricauda ruestringensis	77.8439	258	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	77.7305	238	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313225.1	s__Muricauda sp017313225	77.6802	316	1378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:55,708] [INFO] GTDB search result was written to GCF_004804315.1_ASM480431v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:55,709] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:55,712] [INFO] DFAST_QC result json was written to GCF_004804315.1_ASM480431v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:55,713] [INFO] DFAST_QC completed!
[2024-01-24 13:25:55,713] [INFO] Total running time: 0h1m44s