[2024-01-24 12:22:34,322] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:34,324] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:34,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg3905c9f4-4e03-4d2b-bd9a-721823fa579c/dqc_reference
[2024-01-24 12:22:35,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,674] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,674] [INFO] Running command: gunzip -c /var/lib/cwl/stgff37f1fa-88a5-4a9e-a58d-a506a7082242/GCF_022352215.1_ASM2235221v1_genomic.fna.gz | prodigal -d GCF_022352215.1_ASM2235221v1_genomic.fna/cds.fna -a GCF_022352215.1_ASM2235221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:00,656] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:00,656] [INFO] Task started: HMMsearch
[2024-01-24 12:23:00,656] [INFO] Running command: hmmsearch --tblout GCF_022352215.1_ASM2235221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3905c9f4-4e03-4d2b-bd9a-721823fa579c/dqc_reference/reference_markers.hmm GCF_022352215.1_ASM2235221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:00,973] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:00,975] [INFO] Found 6/6 markers.
[2024-01-24 12:23:01,023] [INFO] Query marker FASTA was written to GCF_022352215.1_ASM2235221v1_genomic.fna/markers.fasta
[2024-01-24 12:23:01,024] [INFO] Task started: Blastn
[2024-01-24 12:23:01,024] [INFO] Running command: blastn -query GCF_022352215.1_ASM2235221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3905c9f4-4e03-4d2b-bd9a-721823fa579c/dqc_reference/reference_markers.fasta -out GCF_022352215.1_ASM2235221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:01,676] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:01,680] [INFO] Selected 18 target genomes.
[2024-01-24 12:23:01,680] [INFO] Target genome list was writen to GCF_022352215.1_ASM2235221v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:01,691] [INFO] Task started: fastANI
[2024-01-24 12:23:01,691] [INFO] Running command: fastANI --query /var/lib/cwl/stgff37f1fa-88a5-4a9e-a58d-a506a7082242/GCF_022352215.1_ASM2235221v1_genomic.fna.gz --refList GCF_022352215.1_ASM2235221v1_genomic.fna/target_genomes.txt --output GCF_022352215.1_ASM2235221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:17,705] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:17,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3905c9f4-4e03-4d2b-bd9a-721823fa579c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:17,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3905c9f4-4e03-4d2b-bd9a-721823fa579c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:17,719] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:17,719] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:17,719] [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
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	100.0	1584	1584	95	conclusive
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	77.8617	356	1584	95	below_threshold
Flavihumibacter profundi	strain=KCTC 62290	GCA_020076305.1	2716883	2716883	type	True	77.4162	221	1584	95	below_threshold
Flavihumibacter petaseus	strain=NBRC 106054	GCA_000974785.1	549295	549295	type	True	77.3334	195	1584	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	77.2805	217	1584	95	below_threshold
Flavihumibacter fluminis	strain=IMCC34837	GCA_018595675.2	2838157	2838157	type	True	77.0238	258	1584	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	76.4754	106	1584	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	76.4097	93	1584	95	below_threshold
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	76.2588	65	1584	95	below_threshold
Sediminibacterium roseum	strain=SYL130	GCA_009939005.1	1978412	1978412	type	True	76.1115	54	1584	95	below_threshold
Flavisolibacter ginsengisoli	strain=DSM 18119	GCA_900129295.1	462367	462367	type	True	75.8895	67	1584	95	below_threshold
Chitinophaga ginsengisegetis	strain=DSM 18108	GCA_900168065.1	393003	393003	type	True	75.8612	59	1584	95	below_threshold
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	75.8482	100	1584	95	below_threshold
Chitinophaga niabensis	strain=DSM 24787	GCA_900129465.1	536979	536979	type	True	75.7607	59	1584	95	below_threshold
Chitinophaga arvensicola	strain=DSM 3695	GCA_900110835.1	29529	29529	type	True	75.5999	68	1584	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:17,721] [INFO] DFAST Taxonomy check result was written to GCF_022352215.1_ASM2235221v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:17,721] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:17,722] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:17,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3905c9f4-4e03-4d2b-bd9a-721823fa579c/dqc_reference/checkm_data
[2024-01-24 12:23:17,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:17,774] [INFO] Task started: CheckM
[2024-01-24 12:23:17,775] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022352215.1_ASM2235221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022352215.1_ASM2235221v1_genomic.fna/checkm_input GCF_022352215.1_ASM2235221v1_genomic.fna/checkm_result
[2024-01-24 12:24:24,909] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:24,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:24,936] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:24,937] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:24,937] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022352215.1_ASM2235221v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:24,938] [INFO] Task started: Blastn
[2024-01-24 12:24:24,938] [INFO] Running command: blastn -query GCF_022352215.1_ASM2235221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3905c9f4-4e03-4d2b-bd9a-721823fa579c/dqc_reference/reference_markers_gtdb.fasta -out GCF_022352215.1_ASM2235221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:25,722] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:25,725] [INFO] Selected 18 target genomes.
[2024-01-24 12:24:25,726] [INFO] Target genome list was writen to GCF_022352215.1_ASM2235221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:25,739] [INFO] Task started: fastANI
[2024-01-24 12:24:25,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgff37f1fa-88a5-4a9e-a58d-a506a7082242/GCF_022352215.1_ASM2235221v1_genomic.fna.gz --refList GCF_022352215.1_ASM2235221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022352215.1_ASM2235221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:40,769] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:40,789] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:24:40,789] [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
GCA_018993145.1	s__Flavihumibacter sp018993145	91.8485	585	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787265.1	s__Flavihumibacter sp016787265	86.46	1220	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483205.1	s__Flavihumibacter sp002483205	80.3846	760	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001601815.1	s__Flavihumibacter sp001601815	79.0868	612	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014332695.1	s__Flavihumibacter stibioxidans	77.8715	355	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814325.1	s__Flavihumibacter sp000814325	77.6198	199	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974785.1	s__Flavihumibacter petaseus	77.3035	197	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018595675.1	s__Flavihumibacter sp018595675	77.0691	256	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759375.1	s__Paraflavitalea devenefica	76.4754	106	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246855.1	s__Niastella koreensis	76.2573	92	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000511175.1	s__Sediminibacterium salmoneum	76.2316	66	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924755.1	s__Niastella sp016924755	76.1059	90	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994055.1	s__Filimonas endophytica	76.0549	59	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110245.1	s__Niastella yeongjuensis	75.9762	90	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011357845.1	s__UBA3961 sp011357845	75.9505	69	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA3961	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786885.1	s__JJ008 sp016786885	75.6001	77	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379905.1	s__Ferruginibacter sp014379905	75.2695	55	1584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:40,791] [INFO] GTDB search result was written to GCF_022352215.1_ASM2235221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:40,791] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:40,795] [INFO] DFAST_QC result json was written to GCF_022352215.1_ASM2235221v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:40,795] [INFO] DFAST_QC completed!
[2024-01-24 12:24:40,795] [INFO] Total running time: 0h2m6s