[2024-01-25 18:02:06,136] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:06,139] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:06,139] [INFO] DQC Reference Directory: /var/lib/cwl/stg416a59f9-af41-4bff-92c8-55204ac6e151/dqc_reference
[2024-01-25 18:02:07,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:07,281] [INFO] Task started: Prodigal
[2024-01-25 18:02:07,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg30c7e146-6a78-4c12-8176-b062f7616904/GCF_002009335.2_ASM200933v2_genomic.fna.gz | prodigal -d GCF_002009335.2_ASM200933v2_genomic.fna/cds.fna -a GCF_002009335.2_ASM200933v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:18,806] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:18,806] [INFO] Task started: HMMsearch
[2024-01-25 18:02:18,806] [INFO] Running command: hmmsearch --tblout GCF_002009335.2_ASM200933v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg416a59f9-af41-4bff-92c8-55204ac6e151/dqc_reference/reference_markers.hmm GCF_002009335.2_ASM200933v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:19,100] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:19,101] [INFO] Found 6/6 markers.
[2024-01-25 18:02:19,147] [INFO] Query marker FASTA was written to GCF_002009335.2_ASM200933v2_genomic.fna/markers.fasta
[2024-01-25 18:02:19,147] [INFO] Task started: Blastn
[2024-01-25 18:02:19,147] [INFO] Running command: blastn -query GCF_002009335.2_ASM200933v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg416a59f9-af41-4bff-92c8-55204ac6e151/dqc_reference/reference_markers.fasta -out GCF_002009335.2_ASM200933v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:19,695] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:19,697] [INFO] Selected 14 target genomes.
[2024-01-25 18:02:19,698] [INFO] Target genome list was writen to GCF_002009335.2_ASM200933v2_genomic.fna/target_genomes.txt
[2024-01-25 18:02:19,704] [INFO] Task started: fastANI
[2024-01-25 18:02:19,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg30c7e146-6a78-4c12-8176-b062f7616904/GCF_002009335.2_ASM200933v2_genomic.fna.gz --refList GCF_002009335.2_ASM200933v2_genomic.fna/target_genomes.txt --output GCF_002009335.2_ASM200933v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:31,861] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:31,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg416a59f9-af41-4bff-92c8-55204ac6e151/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:31,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg416a59f9-af41-4bff-92c8-55204ac6e151/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:31,867] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:02:31,868] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:31,868] [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
Desulfococcus multivorans	strain=DSM 2059	GCA_002009335.2	897	897	type	True	100.0	1483	1485	95	conclusive
Desulfococcus multivorans	strain=DSM 2059	GCA_001854245.1	897	897	type	True	99.9968	1483	1485	95	conclusive
Desulfococcus multivorans	strain=DSM 2059	GCA_900167235.1	897	897	type	True	99.9736	1430	1485	95	conclusive
Desulfococcus multivorans	strain=DSM 2059	GCA_000422185.1	897	897	type	True	99.9424	1389	1485	95	conclusive
Desulfonema ishimotonii	strain=Tokyo 01	GCA_003851005.1	45657	45657	type	True	77.1543	197	1485	95	below_threshold
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	76.8473	122	1485	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:31,869] [INFO] DFAST Taxonomy check result was written to GCF_002009335.2_ASM200933v2_genomic.fna/tc_result.tsv
[2024-01-25 18:02:31,870] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:31,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:31,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg416a59f9-af41-4bff-92c8-55204ac6e151/dqc_reference/checkm_data
[2024-01-25 18:02:31,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:31,917] [INFO] Task started: CheckM
[2024-01-25 18:02:31,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002009335.2_ASM200933v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002009335.2_ASM200933v2_genomic.fna/checkm_input GCF_002009335.2_ASM200933v2_genomic.fna/checkm_result
[2024-01-25 18:03:07,975] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:07,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:07,995] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:07,996] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:07,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002009335.2_ASM200933v2_genomic.fna/markers.fasta)
[2024-01-25 18:03:07,996] [INFO] Task started: Blastn
[2024-01-25 18:03:07,996] [INFO] Running command: blastn -query GCF_002009335.2_ASM200933v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg416a59f9-af41-4bff-92c8-55204ac6e151/dqc_reference/reference_markers_gtdb.fasta -out GCF_002009335.2_ASM200933v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:08,814] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:08,817] [INFO] Selected 28 target genomes.
[2024-01-25 18:03:08,817] [INFO] Target genome list was writen to GCF_002009335.2_ASM200933v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:08,845] [INFO] Task started: fastANI
[2024-01-25 18:03:08,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg30c7e146-6a78-4c12-8176-b062f7616904/GCF_002009335.2_ASM200933v2_genomic.fna.gz --refList GCF_002009335.2_ASM200933v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002009335.2_ASM200933v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:30,458] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:30,468] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:30,468] [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_001854245.1	s__Desulfococcus multivorans	99.9968	1483	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__Desulfococcus	95.0	100.00	99.99	1.00	1.00	4	conclusive
GCA_002327445.1	s__UBA2174 sp002327445	77.0778	128	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA2174;g__UBA2174	95.0	99.95	99.95	0.95	0.95	2	-
GCF_003851005.1	s__Desulfonema_B ishimotonii	77.0564	196	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__Desulfonema_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389855.1	s__JAABTD01 sp011389855	77.0218	174	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390315.1	s__JAABSQ01 sp011390315	76.9807	146	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABSQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009688965.1	s__Desulfosarcina widdelii	76.8569	122	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432195.1	s__UBA5852 sp002432195	76.7959	135	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA5852;g__UBA5852	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009689005.1	s__Desulfosarcina ovata	76.7906	108	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	97.03	97.03	0.77	0.77	2	-
GCF_001311845.1	s__Desulfosarcina cetonica	76.6935	107	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	99.91	99.91	0.98	0.98	2	-
GCA_014237405.1	s__Desulfosarcina sp014237405	76.6077	107	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	99.69	99.69	0.89	0.89	3	-
GCA_011390035.1	s__JAABTE01 sp011390035	76.4463	87	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011328735.1	s__SpSt-501 sp011328735	76.4452	76	1485	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_016342285.1	s__JAEINQ01 sp016342285	76.3617	110	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__JAEINQ01;g__JAEINQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003597945.1	s__SURF-33 sp003597945	76.3238	64	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__SURF-33	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018224455.1	s__Desulfosarcina sp018224455	76.3071	80	1485	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:30,469] [INFO] GTDB search result was written to GCF_002009335.2_ASM200933v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:30,470] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:30,474] [INFO] DFAST_QC result json was written to GCF_002009335.2_ASM200933v2_genomic.fna/dqc_result.json
[2024-01-25 18:03:30,474] [INFO] DFAST_QC completed!
[2024-01-25 18:03:30,474] [INFO] Total running time: 0h1m24s