[2024-01-25 20:20:05,918] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:05,920] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:05,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f567688-a7fb-4133-ae5b-88d45dc36c50/dqc_reference
[2024-01-25 20:20:07,099] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:07,100] [INFO] Task started: Prodigal
[2024-01-25 20:20:07,100] [INFO] Running command: gunzip -c /var/lib/cwl/stg614a0dc9-0acb-4cc7-8152-9d59683ca9e6/GCF_000719975.1_ASM71997v1_genomic.fna.gz | prodigal -d GCF_000719975.1_ASM71997v1_genomic.fna/cds.fna -a GCF_000719975.1_ASM71997v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:21,352] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:21,353] [INFO] Task started: HMMsearch
[2024-01-25 20:20:21,353] [INFO] Running command: hmmsearch --tblout GCF_000719975.1_ASM71997v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f567688-a7fb-4133-ae5b-88d45dc36c50/dqc_reference/reference_markers.hmm GCF_000719975.1_ASM71997v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:21,640] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:21,641] [INFO] Found 6/6 markers.
[2024-01-25 20:20:21,682] [INFO] Query marker FASTA was written to GCF_000719975.1_ASM71997v1_genomic.fna/markers.fasta
[2024-01-25 20:20:21,682] [INFO] Task started: Blastn
[2024-01-25 20:20:21,682] [INFO] Running command: blastn -query GCF_000719975.1_ASM71997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f567688-a7fb-4133-ae5b-88d45dc36c50/dqc_reference/reference_markers.fasta -out GCF_000719975.1_ASM71997v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:22,999] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:23,002] [INFO] Selected 17 target genomes.
[2024-01-25 20:20:23,002] [INFO] Target genome list was writen to GCF_000719975.1_ASM71997v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:23,035] [INFO] Task started: fastANI
[2024-01-25 20:20:23,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg614a0dc9-0acb-4cc7-8152-9d59683ca9e6/GCF_000719975.1_ASM71997v1_genomic.fna.gz --refList GCF_000719975.1_ASM71997v1_genomic.fna/target_genomes.txt --output GCF_000719975.1_ASM71997v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:46,306] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:46,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f567688-a7fb-4133-ae5b-88d45dc36c50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:46,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f567688-a7fb-4133-ae5b-88d45dc36c50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:46,317] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:20:46,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:46,318] [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
Prauserella rugosa	strain=NRRL B-2295	GCA_000719975.1	43354	43354	type	True	100.0	1700	1704	95	conclusive
Prauserella rugosa	strain=DSM 43194	GCA_007829565.1	43354	43354	type	True	99.9961	1704	1704	95	conclusive
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	84.3837	1279	1704	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	84.1696	1292	1704	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.4575	980	1704	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	80.3756	928	1704	95	below_threshold
Saccharomonospora iraqiensis	strain=IQ-H1	GCA_000430445.1	52698	52698	type	True	79.7892	588	1704	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.7206	787	1704	95	below_threshold
Amycolatopsis granulosa	strain=DSM 45669	GCA_011758745.1	185684	185684	type	True	79.5132	725	1704	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	79.415	765	1704	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	79.377	752	1704	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.8467	789	1704	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	78.7164	746	1704	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	78.6889	755	1704	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	77.5888	579	1704	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	77.1997	506	1704	95	below_threshold
Pseudonocardia alaniniphila	strain=Y-16303	GCA_022524485.1	75291	75291	type	True	77.0534	499	1704	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:46,319] [INFO] DFAST Taxonomy check result was written to GCF_000719975.1_ASM71997v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:46,324] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:46,324] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:46,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f567688-a7fb-4133-ae5b-88d45dc36c50/dqc_reference/checkm_data
[2024-01-25 20:20:46,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:46,374] [INFO] Task started: CheckM
[2024-01-25 20:20:46,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000719975.1_ASM71997v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000719975.1_ASM71997v1_genomic.fna/checkm_input GCF_000719975.1_ASM71997v1_genomic.fna/checkm_result
[2024-01-25 20:22:10,536] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:10,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:10,581] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:10,581] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:10,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000719975.1_ASM71997v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:10,583] [INFO] Task started: Blastn
[2024-01-25 20:22:10,583] [INFO] Running command: blastn -query GCF_000719975.1_ASM71997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f567688-a7fb-4133-ae5b-88d45dc36c50/dqc_reference/reference_markers_gtdb.fasta -out GCF_000719975.1_ASM71997v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:12,707] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:12,710] [INFO] Selected 17 target genomes.
[2024-01-25 20:22:12,710] [INFO] Target genome list was writen to GCF_000719975.1_ASM71997v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:12,727] [INFO] Task started: fastANI
[2024-01-25 20:22:12,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg614a0dc9-0acb-4cc7-8152-9d59683ca9e6/GCF_000719975.1_ASM71997v1_genomic.fna.gz --refList GCF_000719975.1_ASM71997v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000719975.1_ASM71997v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:35,596] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:35,608] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:35,609] [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_000719975.1	s__Saccharomonospora rugosa	100.0	1700	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.54	99.08	0.98	0.95	3	conclusive
GCF_001942305.1	s__Saccharomonospora sp001942305	86.1211	1263	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191605.1	s__Saccharomonospora isguenensis	84.1859	1289	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195435.1	s__Saccharomonospora sediminis	83.9495	1251	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202235.1	s__Saccharomonospora sp003202235	80.5491	1008	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595675.1	s__Saccharomonospora sp016595675	80.4709	977	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005146945.1	s__Saccharomonospora endophytica	80.4475	961	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_000430445.1	s__Saccharomonospora iraqiensis	79.7853	588	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	96.0038	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	79.3607	753	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002262875.1	s__Amycolatopsis antarctica	79.0423	695	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018885265.1	s__Amycolatopsis_D sp018885265	78.8032	747	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001995215.1	s__Amycolatopsis azurea	78.7164	750	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014654365.1	s__Amycolatopsis oliviviridis	78.7134	760	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826545.1	s__Kibdelosporangium sp000826545	77.4251	578	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539565.1	s__Pseudonocardia hydrocarbonoxydans	77.189	511	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933465.1	s__Actinomycetospora sp012933465	76.7993	500	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289575.1	s__Dietzia natronolimnaea_A	76.5996	214	1704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	96.66	96.66	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:35,610] [INFO] GTDB search result was written to GCF_000719975.1_ASM71997v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:35,612] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:35,615] [INFO] DFAST_QC result json was written to GCF_000719975.1_ASM71997v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:35,615] [INFO] DFAST_QC completed!
[2024-01-25 20:22:35,615] [INFO] Total running time: 0h2m30s