[2024-01-25 18:20:20,765] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:20:20,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:20:20,767] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe2fd781-323f-4b28-86d2-9281df994a56/dqc_reference
[2024-01-25 18:20:21,948] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:20:21,949] [INFO] Task started: Prodigal
[2024-01-25 18:20:21,949] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e5a98c8-6fde-44e9-8956-dcf6f49d2bcd/GCF_009733845.1_ASM973384v1_genomic.fna.gz | prodigal -d GCF_009733845.1_ASM973384v1_genomic.fna/cds.fna -a GCF_009733845.1_ASM973384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:20:34,393] [INFO] Task succeeded: Prodigal
[2024-01-25 18:20:34,394] [INFO] Task started: HMMsearch
[2024-01-25 18:20:34,394] [INFO] Running command: hmmsearch --tblout GCF_009733845.1_ASM973384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe2fd781-323f-4b28-86d2-9281df994a56/dqc_reference/reference_markers.hmm GCF_009733845.1_ASM973384v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:20:34,657] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:20:34,658] [INFO] Found 6/6 markers.
[2024-01-25 18:20:34,697] [INFO] Query marker FASTA was written to GCF_009733845.1_ASM973384v1_genomic.fna/markers.fasta
[2024-01-25 18:20:34,697] [INFO] Task started: Blastn
[2024-01-25 18:20:34,697] [INFO] Running command: blastn -query GCF_009733845.1_ASM973384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe2fd781-323f-4b28-86d2-9281df994a56/dqc_reference/reference_markers.fasta -out GCF_009733845.1_ASM973384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:35,843] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:35,850] [INFO] Selected 19 target genomes.
[2024-01-25 18:20:35,850] [INFO] Target genome list was writen to GCF_009733845.1_ASM973384v1_genomic.fna/target_genomes.txt
[2024-01-25 18:20:35,862] [INFO] Task started: fastANI
[2024-01-25 18:20:35,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e5a98c8-6fde-44e9-8956-dcf6f49d2bcd/GCF_009733845.1_ASM973384v1_genomic.fna.gz --refList GCF_009733845.1_ASM973384v1_genomic.fna/target_genomes.txt --output GCF_009733845.1_ASM973384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:20:52,472] [INFO] Task succeeded: fastANI
[2024-01-25 18:20:52,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe2fd781-323f-4b28-86d2-9281df994a56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:20:52,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe2fd781-323f-4b28-86d2-9281df994a56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:20:52,485] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:20:52,485] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:20:52,485] [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 terrae	strain=KACC 16542	GCA_009733845.1	1743262	1743262	type	True	100.0	1575	1577	95	conclusive
Pseudactinotalea suaedae	strain=KACC 17839	GCA_009733815.1	1524924	1524924	type	True	84.524	1085	1577	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	78.8571	597	1577	95	below_threshold
Occultella kanbiaonis	strain=HY164	GCA_009708215.1	2675754	2675754	type	True	78.8427	625	1577	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	78.7094	605	1577	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	78.7024	622	1577	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	78.6251	496	1577	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	78.1038	426	1577	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	78.083	397	1577	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.8932	413	1577	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	77.8892	409	1577	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	77.8269	391	1577	95	below_threshold
Georgenia thermotolerans	strain=DSM 21501	GCA_009299305.1	527326	527326	type	True	77.8007	407	1577	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	77.7993	417	1577	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	77.7853	413	1577	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	77.736	413	1577	95	below_threshold
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	77.707	430	1577	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	77.6145	401	1577	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	75.8646	326	1577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:20:52,486] [INFO] DFAST Taxonomy check result was written to GCF_009733845.1_ASM973384v1_genomic.fna/tc_result.tsv
[2024-01-25 18:20:52,487] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:20:52,487] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:20:52,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe2fd781-323f-4b28-86d2-9281df994a56/dqc_reference/checkm_data
[2024-01-25 18:20:52,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:20:52,533] [INFO] Task started: CheckM
[2024-01-25 18:20:52,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009733845.1_ASM973384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009733845.1_ASM973384v1_genomic.fna/checkm_input GCF_009733845.1_ASM973384v1_genomic.fna/checkm_result
[2024-01-25 18:22:06,840] [INFO] Task succeeded: CheckM
[2024-01-25 18:22:06,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 18:22:06,868] [INFO] ===== Completeness check finished =====
[2024-01-25 18:22:06,868] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:22:06,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009733845.1_ASM973384v1_genomic.fna/markers.fasta)
[2024-01-25 18:22:06,869] [INFO] Task started: Blastn
[2024-01-25 18:22:06,869] [INFO] Running command: blastn -query GCF_009733845.1_ASM973384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe2fd781-323f-4b28-86d2-9281df994a56/dqc_reference/reference_markers_gtdb.fasta -out GCF_009733845.1_ASM973384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:22:08,709] [INFO] Task succeeded: Blastn
[2024-01-25 18:22:08,712] [INFO] Selected 17 target genomes.
[2024-01-25 18:22:08,712] [INFO] Target genome list was writen to GCF_009733845.1_ASM973384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:22:08,736] [INFO] Task started: fastANI
[2024-01-25 18:22:08,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e5a98c8-6fde-44e9-8956-dcf6f49d2bcd/GCF_009733845.1_ASM973384v1_genomic.fna.gz --refList GCF_009733845.1_ASM973384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009733845.1_ASM973384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:22:24,293] [INFO] Task succeeded: fastANI
[2024-01-25 18:22:24,303] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:22:24,304] [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_009733845.1	s__Pseudactinotalea terrae	100.0	1573	1577	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	84.517	1086	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733795.1	s__Pseudactinotalea caeni	82.3541	894	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708215.1	s__Occultella sp009708215	78.8406	621	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	97.28	97.28	0.86	0.86	2	-
GCF_902703175.1	s__Occultella aeris	78.7304	602	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353825.1	s__Occultella glacieicola	78.6903	625	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000995.1	s__Ruania sp008000995	78.1037	426	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	99.97	99.97	0.98	0.98	2	-
GCF_011603975.1	s__Cellulomonas sp011603975	78.0865	402	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009660225.1	s__HY158 sp009660225	78.0617	379	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__HY158	95.0	98.70	98.70	0.90	0.90	2	-
GCF_006349365.1	s__Oceanitalea sp006349365	77.9509	406	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	99.20	99.20	0.95	0.95	2	-
GCF_009193175.1	s__Georgenia ruanii	77.8094	410	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526515.1	s__Actinotalea sp000526515	77.8042	355	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193185.1	s__Georgenia thermotolerans	77.7819	419	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009193155.1	s__Georgenia subflava	77.7215	428	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009429125.1	s__Luteimicrobium xylanilyticum	77.7205	361	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Luteimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679345.1	s__Cellulomonas cellulans_A	77.7066	439	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659635.1	s__Spirillospora roseirufa	75.8561	328	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:22:24,305] [INFO] GTDB search result was written to GCF_009733845.1_ASM973384v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:22:24,306] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:22:24,311] [INFO] DFAST_QC result json was written to GCF_009733845.1_ASM973384v1_genomic.fna/dqc_result.json
[2024-01-25 18:22:24,312] [INFO] DFAST_QC completed!
[2024-01-25 18:22:24,312] [INFO] Total running time: 0h2m4s