[2024-01-24 13:48:59,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e839381-b37c-4249-b124-1a10735f4ceb/dqc_reference
[2024-01-24 13:49:00,982] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:00,983] [INFO] Task started: Prodigal
[2024-01-24 13:49:00,983] [INFO] Running command: gunzip -c /var/lib/cwl/stge1814822-fed4-4867-b20d-00714ea4c9b0/GCF_018595685.2_ASM1859568v2_genomic.fna.gz | prodigal -d GCF_018595685.2_ASM1859568v2_genomic.fna/cds.fna -a GCF_018595685.2_ASM1859568v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:27,757] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:27,757] [INFO] Task started: HMMsearch
[2024-01-24 13:49:27,757] [INFO] Running command: hmmsearch --tblout GCF_018595685.2_ASM1859568v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e839381-b37c-4249-b124-1a10735f4ceb/dqc_reference/reference_markers.hmm GCF_018595685.2_ASM1859568v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:28,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:28,076] [INFO] Found 6/6 markers.
[2024-01-24 13:49:28,118] [INFO] Query marker FASTA was written to GCF_018595685.2_ASM1859568v2_genomic.fna/markers.fasta
[2024-01-24 13:49:28,119] [INFO] Task started: Blastn
[2024-01-24 13:49:28,119] [INFO] Running command: blastn -query GCF_018595685.2_ASM1859568v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e839381-b37c-4249-b124-1a10735f4ceb/dqc_reference/reference_markers.fasta -out GCF_018595685.2_ASM1859568v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:28,725] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:28,730] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:28,731] [INFO] Target genome list was writen to GCF_018595685.2_ASM1859568v2_genomic.fna/target_genomes.txt
[2024-01-24 13:49:28,739] [INFO] Task started: fastANI
[2024-01-24 13:49:28,739] [INFO] Running command: fastANI --query /var/lib/cwl/stge1814822-fed4-4867-b20d-00714ea4c9b0/GCF_018595685.2_ASM1859568v2_genomic.fna.gz --refList GCF_018595685.2_ASM1859568v2_genomic.fna/target_genomes.txt --output GCF_018595685.2_ASM1859568v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:47,603] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:47,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e839381-b37c-4249-b124-1a10735f4ceb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:47,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e839381-b37c-4249-b124-1a10735f4ceb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:47,627] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:47,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:47,627] [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 rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	100.0	1431	1432	95	conclusive
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	77.7808	333	1432	95	below_threshold
Flavihumibacter solisilvae	strain=3-3	GCA_000814475.1	1349421	1349421	type	True	77.4472	221	1432	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	77.255	218	1432	95	below_threshold
Flavihumibacter profundi	strain=KCTC 62290	GCA_020076305.1	2716883	2716883	type	True	77.1076	191	1432	95	below_threshold
Flavihumibacter fluminis	strain=IMCC34837	GCA_018595675.2	2838157	2838157	type	True	77.0259	228	1432	95	below_threshold
Sediminibacterium roseum	strain=SYL130	GCA_009939005.1	1978412	1978412	type	True	76.5911	69	1432	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	76.5033	141	1432	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	76.4523	125	1432	95	below_threshold
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	76.35	136	1432	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	76.2623	67	1432	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	76.2346	68	1432	95	below_threshold
Terrimonas ferruginea	strain=DSM 30193	GCA_000425585.1	249	249	type	True	76.2082	82	1432	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	76.1338	103	1432	95	below_threshold
Chitinophaga silvisoli	strain=K20C18050901	GCA_003412465.1	2291814	2291814	type	True	76.0769	80	1432	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	75.9664	106	1432	95	below_threshold
Chitinophaga tropicalis	strain=ysch24	GCA_009758205.1	2683588	2683588	type	True	75.9431	60	1432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:47,631] [INFO] DFAST Taxonomy check result was written to GCF_018595685.2_ASM1859568v2_genomic.fna/tc_result.tsv
[2024-01-24 13:49:47,631] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:47,632] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:47,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e839381-b37c-4249-b124-1a10735f4ceb/dqc_reference/checkm_data
[2024-01-24 13:49:47,633] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:47,685] [INFO] Task started: CheckM
[2024-01-24 13:49:47,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018595685.2_ASM1859568v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018595685.2_ASM1859568v2_genomic.fna/checkm_input GCF_018595685.2_ASM1859568v2_genomic.fna/checkm_result
[2024-01-24 13:51:00,821] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:00,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:00,842] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:00,842] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:00,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018595685.2_ASM1859568v2_genomic.fna/markers.fasta)
[2024-01-24 13:51:00,843] [INFO] Task started: Blastn
[2024-01-24 13:51:00,843] [INFO] Running command: blastn -query GCF_018595685.2_ASM1859568v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e839381-b37c-4249-b124-1a10735f4ceb/dqc_reference/reference_markers_gtdb.fasta -out GCF_018595685.2_ASM1859568v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:01,649] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:01,653] [INFO] Selected 19 target genomes.
[2024-01-24 13:51:01,654] [INFO] Target genome list was writen to GCF_018595685.2_ASM1859568v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:01,693] [INFO] Task started: fastANI
[2024-01-24 13:51:01,694] [INFO] Running command: fastANI --query /var/lib/cwl/stge1814822-fed4-4867-b20d-00714ea4c9b0/GCF_018595685.2_ASM1859568v2_genomic.fna.gz --refList GCF_018595685.2_ASM1859568v2_genomic.fna/target_genomes_gtdb.txt --output GCF_018595685.2_ASM1859568v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:18,758] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:18,777] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:18,778] [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_018595685.1	s__Flavihumibacter sp018595685	99.9865	1415	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014332695.1	s__Flavihumibacter stibioxidans	77.7808	333	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814475.1	s__Flavihumibacter solisilvae	77.4502	220	1432	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	77.2217	202	1432	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	77.1958	200	1432	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	77.0795	209	1432	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	77.0109	224	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018993145.1	s__Flavihumibacter sp018993145	76.8951	98	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001302245.1	s__PMP191F sp001302245	76.7991	103	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__PMP191F	95.0	99.37	99.37	0.95	0.95	2	-
GCF_011759375.1	s__Paraflavitalea devenefica	76.5033	141	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849455.1	s__Pseudobacter sp017849455	76.2944	138	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425585.1	s__Terrimonas ferruginea	76.2224	80	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Terrimonas	95.0	95.38	95.33	0.94	0.93	4	-
GCA_016192105.1	s__JJ008 sp016192105	76.1361	90	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003412465.1	s__Chitinophaga silvisoli	76.0769	80	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744515.1	s__Paraflavitalea sp017744515	76.0727	119	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655015.1	s__Puia sp015655015	75.8683	84	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906365.1	s__Puia sp903906365	75.8474	83	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	99.91	99.90	0.99	0.98	4	-
GCA_014879565.1	s__JJ008 sp014879565	75.8381	77	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:18,779] [INFO] GTDB search result was written to GCF_018595685.2_ASM1859568v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:18,780] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:18,784] [INFO] DFAST_QC result json was written to GCF_018595685.2_ASM1859568v2_genomic.fna/dqc_result.json
[2024-01-24 13:51:18,784] [INFO] DFAST_QC completed!
[2024-01-24 13:51:18,784] [INFO] Total running time: 0h2m19s