[2024-01-24 12:54:22,082] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:22,085] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:22,085] [INFO] DQC Reference Directory: /var/lib/cwl/stg4aba1ce3-caaa-41c6-86b2-b11c029a66d1/dqc_reference
[2024-01-24 12:54:23,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:23,878] [INFO] Task started: Prodigal
[2024-01-24 12:54:23,878] [INFO] Running command: gunzip -c /var/lib/cwl/stge88e8fe9-a68b-406a-ba1f-9a3d2101bc1d/GCF_009733795.1_ASM973379v1_genomic.fna.gz | prodigal -d GCF_009733795.1_ASM973379v1_genomic.fna/cds.fna -a GCF_009733795.1_ASM973379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:34,427] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:34,427] [INFO] Task started: HMMsearch
[2024-01-24 12:54:34,427] [INFO] Running command: hmmsearch --tblout GCF_009733795.1_ASM973379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4aba1ce3-caaa-41c6-86b2-b11c029a66d1/dqc_reference/reference_markers.hmm GCF_009733795.1_ASM973379v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:34,728] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:34,730] [INFO] Found 6/6 markers.
[2024-01-24 12:54:34,770] [INFO] Query marker FASTA was written to GCF_009733795.1_ASM973379v1_genomic.fna/markers.fasta
[2024-01-24 12:54:34,770] [INFO] Task started: Blastn
[2024-01-24 12:54:34,770] [INFO] Running command: blastn -query GCF_009733795.1_ASM973379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4aba1ce3-caaa-41c6-86b2-b11c029a66d1/dqc_reference/reference_markers.fasta -out GCF_009733795.1_ASM973379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:36,263] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:36,268] [INFO] Selected 26 target genomes.
[2024-01-24 12:54:36,269] [INFO] Target genome list was writen to GCF_009733795.1_ASM973379v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:36,279] [INFO] Task started: fastANI
[2024-01-24 12:54:36,279] [INFO] Running command: fastANI --query /var/lib/cwl/stge88e8fe9-a68b-406a-ba1f-9a3d2101bc1d/GCF_009733795.1_ASM973379v1_genomic.fna.gz --refList GCF_009733795.1_ASM973379v1_genomic.fna/target_genomes.txt --output GCF_009733795.1_ASM973379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:59,911] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:59,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4aba1ce3-caaa-41c6-86b2-b11c029a66d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:59,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4aba1ce3-caaa-41c6-86b2-b11c029a66d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:59,938] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:54:59,939] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:54:59,939] [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
Pseudactinotalea suaedae	strain=KACC 17839	GCA_009733815.1	1524924	1524924	type	True	82.5331	923	1309	95	below_threshold
Pseudactinotalea terrae	strain=KACC 16542	GCA_009733845.1	1743262	1743262	type	True	82.3102	889	1309	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	78.7872	590	1309	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	78.7758	617	1309	95	below_threshold
Occultella kanbiaonis	strain=HY164	GCA_009708215.1	2675754	2675754	type	True	78.7331	629	1309	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	78.6745	627	1309	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	78.4225	487	1309	95	below_threshold
Ruania albidiflava	strain=DSM 18029	GCA_000421225.1	366586	366586	type	True	78.2184	494	1309	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	78.1877	502	1309	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	78.1809	511	1309	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	78.1539	477	1309	95	below_threshold
Ruania alba	strain=DSM 21368	GCA_900105765.1	648782	648782	type	True	78.1189	448	1309	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	78.0902	381	1309	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	78.0862	523	1309	95	below_threshold
Cellulomonas timonensis	strain=SN7	GCA_900046455.1	1689271	1689271	type	True	78.0277	436	1309	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	78.0249	563	1309	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	78.0194	482	1309	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	77.9995	592	1309	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	77.9423	492	1309	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	77.9362	514	1309	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	77.9122	559	1309	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	77.8996	577	1309	95	below_threshold
Cellulomonas carbonis	strain=CGMCC 1.10786	GCA_014636275.1	1386092	1386092	type	True	77.8719	545	1309	95	below_threshold
Paraoerskovia marina	strain=DSM 21750	GCA_000701465.1	545619	545619	type	True	77.6292	371	1309	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	76.486	431	1309	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	76.178	493	1309	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:59,941] [INFO] DFAST Taxonomy check result was written to GCF_009733795.1_ASM973379v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:59,941] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:59,942] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:59,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4aba1ce3-caaa-41c6-86b2-b11c029a66d1/dqc_reference/checkm_data
[2024-01-24 12:54:59,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:59,988] [INFO] Task started: CheckM
[2024-01-24 12:54:59,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009733795.1_ASM973379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009733795.1_ASM973379v1_genomic.fna/checkm_input GCF_009733795.1_ASM973379v1_genomic.fna/checkm_result
[2024-01-24 12:55:54,830] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:54,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:54,852] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:54,852] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:54,853] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009733795.1_ASM973379v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:54,853] [INFO] Task started: Blastn
[2024-01-24 12:55:54,853] [INFO] Running command: blastn -query GCF_009733795.1_ASM973379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4aba1ce3-caaa-41c6-86b2-b11c029a66d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_009733795.1_ASM973379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:57,395] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:57,398] [INFO] Selected 20 target genomes.
[2024-01-24 12:55:57,398] [INFO] Target genome list was writen to GCF_009733795.1_ASM973379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:57,432] [INFO] Task started: fastANI
[2024-01-24 12:55:57,432] [INFO] Running command: fastANI --query /var/lib/cwl/stge88e8fe9-a68b-406a-ba1f-9a3d2101bc1d/GCF_009733795.1_ASM973379v1_genomic.fna.gz --refList GCF_009733795.1_ASM973379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009733795.1_ASM973379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:18,217] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:18,238] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:18,238] [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_009733795.1	s__Pseudactinotalea caeni	100.0	1307	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009733815.1	s__Pseudactinotalea suaedae	82.5594	920	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733845.1	s__Pseudactinotalea terrae	82.3148	890	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353825.1	s__Occultella glacieicola	78.7821	590	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396155.1	s__Cellulomonas septica	78.5438	392	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215105.1	s__Isoptericola variabilis_A	78.5332	520	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_009660225.1	s__HY158 sp009660225	78.5035	446	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__HY158	95.0	98.70	98.70	0.90	0.90	2	-
GCA_014837105.1	s__Oceanitalea sp014837105	78.4845	479	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751805.1	s__Salana multivorans	78.3025	496	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Salana	95.0	99.05	99.05	0.93	0.93	2	-
GCF_900116375.1	s__Oceanitalea nanhaiensis	78.2774	474	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011603975.1	s__Cellulomonas sp011603975	78.2372	497	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421225.1	s__Ruania albidiflava	78.2337	492	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239125.1	s__Cellulomonas hominis_A	78.187	514	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814705.1	s__Georgenia muralis	78.1367	483	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797595.1	s__Sediminihabitans luteus	78.0662	526	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007679345.1	s__Cellulomonas cellulans_A	78.0085	572	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636275.1	s__Actinotalea carbonis	77.9059	540	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	100.00	100.00	0.97	0.97	2	-
GCF_011634835.1	s__Isoptericola sp011634835	77.7764	551	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003001795.1	s__Actinomadura_B viridilutea	76.4956	441	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013364275.1	s__Spirillospora sp013364275	76.2241	542	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:18,240] [INFO] GTDB search result was written to GCF_009733795.1_ASM973379v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:18,240] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:18,245] [INFO] DFAST_QC result json was written to GCF_009733795.1_ASM973379v1_genomic.fna/dqc_result.json
[2024-01-24 12:56:18,245] [INFO] DFAST_QC completed!
[2024-01-24 12:56:18,245] [INFO] Total running time: 0h1m56s