[2023-07-01 01:53:49,869] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:53:49,872] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:53:49,872] [INFO] DQC Reference Directory: /var/lib/cwl/stgf49ac489-1dc7-4d72-9263-59eaf14ebcc4/dqc_reference
[2023-07-01 01:53:51,126] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:53:51,126] [INFO] Task started: Prodigal
[2023-07-01 01:53:51,127] [INFO] Running command: gunzip -c /var/lib/cwl/stg1be76837-1c18-4222-85c9-8e22cda74f8f/GCA_016183025.1_ASM1618302v1_genomic.fna.gz | prodigal -d GCA_016183025.1_ASM1618302v1_genomic.fna/cds.fna -a GCA_016183025.1_ASM1618302v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:54:00,107] [INFO] Task succeeded: Prodigal
[2023-07-01 01:54:00,108] [INFO] Task started: HMMsearch
[2023-07-01 01:54:00,108] [INFO] Running command: hmmsearch --tblout GCA_016183025.1_ASM1618302v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf49ac489-1dc7-4d72-9263-59eaf14ebcc4/dqc_reference/reference_markers.hmm GCA_016183025.1_ASM1618302v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:54:00,448] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:54:00,450] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1be76837-1c18-4222-85c9-8e22cda74f8f/GCA_016183025.1_ASM1618302v1_genomic.fna.gz]
[2023-07-01 01:54:00,491] [INFO] Query marker FASTA was written to GCA_016183025.1_ASM1618302v1_genomic.fna/markers.fasta
[2023-07-01 01:54:00,491] [INFO] Task started: Blastn
[2023-07-01 01:54:00,492] [INFO] Running command: blastn -query GCA_016183025.1_ASM1618302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf49ac489-1dc7-4d72-9263-59eaf14ebcc4/dqc_reference/reference_markers.fasta -out GCA_016183025.1_ASM1618302v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:54:01,164] [INFO] Task succeeded: Blastn
[2023-07-01 01:54:01,168] [INFO] Selected 24 target genomes.
[2023-07-01 01:54:01,168] [INFO] Target genome list was writen to GCA_016183025.1_ASM1618302v1_genomic.fna/target_genomes.txt
[2023-07-01 01:54:01,172] [INFO] Task started: fastANI
[2023-07-01 01:54:01,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg1be76837-1c18-4222-85c9-8e22cda74f8f/GCA_016183025.1_ASM1618302v1_genomic.fna.gz --refList GCA_016183025.1_ASM1618302v1_genomic.fna/target_genomes.txt --output GCA_016183025.1_ASM1618302v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:54:21,641] [INFO] Task succeeded: fastANI
[2023-07-01 01:54:21,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf49ac489-1dc7-4d72-9263-59eaf14ebcc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:54:21,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf49ac489-1dc7-4d72-9263-59eaf14ebcc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:54:21,651] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:54:21,652] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 01:54:21,652] [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
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	75.414	59	1087	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1726	121	1087	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	75.0665	110	1087	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	75.0606	111	1087	95	below_threshold
Thermaerobacter subterraneus	strain=DSM 13965	GCA_000183545.3	175696	175696	type	True	75.0477	81	1087	95	below_threshold
Corallococcus interemptor	strain=AB047A	GCA_003668875.1	2316720	2316720	type	True	75.045	92	1087	95	below_threshold
Corallococcus exiguus	strain=DSM 14696	GCA_009909105.1	83462	83462	type	True	74.9722	96	1087	95	below_threshold
Corallococcus coralloides	strain=DSM 2259	GCA_000255295.1	184914	184914	type	True	74.9718	98	1087	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	74.809	72	1087	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	74.7372	67	1087	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	74.6875	84	1087	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 01:54:21,654] [INFO] DFAST Taxonomy check result was written to GCA_016183025.1_ASM1618302v1_genomic.fna/tc_result.tsv
[2023-07-01 01:54:21,655] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:54:21,655] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:54:21,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf49ac489-1dc7-4d72-9263-59eaf14ebcc4/dqc_reference/checkm_data
[2023-07-01 01:54:21,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:54:21,696] [INFO] Task started: CheckM
[2023-07-01 01:54:21,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016183025.1_ASM1618302v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016183025.1_ASM1618302v1_genomic.fna/checkm_input GCA_016183025.1_ASM1618302v1_genomic.fna/checkm_result
[2023-07-01 01:54:53,289] [INFO] Task succeeded: CheckM
[2023-07-01 01:54:53,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 01:54:53,311] [INFO] ===== Completeness check finished =====
[2023-07-01 01:54:53,312] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:54:53,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016183025.1_ASM1618302v1_genomic.fna/markers.fasta)
[2023-07-01 01:54:53,312] [INFO] Task started: Blastn
[2023-07-01 01:54:53,312] [INFO] Running command: blastn -query GCA_016183025.1_ASM1618302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf49ac489-1dc7-4d72-9263-59eaf14ebcc4/dqc_reference/reference_markers_gtdb.fasta -out GCA_016183025.1_ASM1618302v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:54:54,197] [INFO] Task succeeded: Blastn
[2023-07-01 01:54:54,202] [INFO] Selected 20 target genomes.
[2023-07-01 01:54:54,202] [INFO] Target genome list was writen to GCA_016183025.1_ASM1618302v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:54:54,230] [INFO] Task started: fastANI
[2023-07-01 01:54:54,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg1be76837-1c18-4222-85c9-8e22cda74f8f/GCA_016183025.1_ASM1618302v1_genomic.fna.gz --refList GCA_016183025.1_ASM1618302v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016183025.1_ASM1618302v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:55:05,804] [INFO] Task succeeded: fastANI
[2023-07-01 01:55:05,818] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 01:55:05,818] [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_016183025.1	s__JACPFL01 sp016183025	100.0	1069	1087	d__Bacteria;p__Desulfobacterota;c__JACPFL01;o__JACPFL01;f__JACPFL01;g__JACPFL01	95.0	99.13	99.13	0.84	0.84	2	conclusive
GCA_016209385.1	s__JACQWB01 sp016209385	77.3723	94	1087	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__JACQWB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016179965.1	s__CSP1-6 sp016179965	76.0157	86	1087	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__CSP1-6	95.0	98.97	98.97	0.88	0.88	2	-
GCA_002011835.1	s__JdFR-95 sp002011835	75.7403	59	1087	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__JdFR-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011058515.1	s__DSHD01 sp011058515	75.7031	100	1087	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__DSHD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018986915.1	s__Geomonas sp018986915	75.4569	55	1087	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011328735.1	s__SpSt-501 sp011328735	75.4215	68	1087	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA2174_A;g__SpSt-501	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005774545.1	s__VAUL01 sp005774545	75.3875	54	1087	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM103;g__VAUL01	95.0	99.97	99.97	0.96	0.96	2	-
GCA_005879315.1	s__40CM-4-68-19 sp005879315	75.3082	55	1087	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__40CM-4-68-19;g__40CM-4-68-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001788495.1	s__GWA2-73-35 sp001788495	75.2819	104	1087	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__GWA2-73-35	95.0	99.58	99.46	0.87	0.84	4	-
GCA_003818285.1	s__RPRB01 sp003818285	75.1136	91	1087	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__RPRB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195325.1	s__JACPZX01 sp016195325	74.945	58	1087	d__Bacteria;p__Acidobacteriota;c__Mor1;o__JACPZX01;f__JACPZX01;g__JACPZX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 01:55:05,820] [INFO] GTDB search result was written to GCA_016183025.1_ASM1618302v1_genomic.fna/result_gtdb.tsv
[2023-07-01 01:55:05,821] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:55:05,833] [INFO] DFAST_QC result json was written to GCA_016183025.1_ASM1618302v1_genomic.fna/dqc_result.json
[2023-07-01 01:55:05,834] [INFO] DFAST_QC completed!
[2023-07-01 01:55:05,834] [INFO] Total running time: 0h1m16s