[2024-01-24 13:22:25,468] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:25,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:25,469] [INFO] DQC Reference Directory: /var/lib/cwl/stgdde1b22a-b1bc-4485-b435-ca1396ebfaa8/dqc_reference
[2024-01-24 13:22:26,629] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:26,632] [INFO] Task started: Prodigal
[2024-01-24 13:22:26,633] [INFO] Running command: gunzip -c /var/lib/cwl/stgbed84822-a8cf-48e8-9fa7-d1df541ce68d/GCF_003851005.1_ASM385100v1_genomic.fna.gz | prodigal -d GCF_003851005.1_ASM385100v1_genomic.fna/cds.fna -a GCF_003851005.1_ASM385100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:43,987] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:43,988] [INFO] Task started: HMMsearch
[2024-01-24 13:22:43,988] [INFO] Running command: hmmsearch --tblout GCF_003851005.1_ASM385100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdde1b22a-b1bc-4485-b435-ca1396ebfaa8/dqc_reference/reference_markers.hmm GCF_003851005.1_ASM385100v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:44,290] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:44,291] [INFO] Found 6/6 markers.
[2024-01-24 13:22:44,337] [INFO] Query marker FASTA was written to GCF_003851005.1_ASM385100v1_genomic.fna/markers.fasta
[2024-01-24 13:22:44,337] [INFO] Task started: Blastn
[2024-01-24 13:22:44,337] [INFO] Running command: blastn -query GCF_003851005.1_ASM385100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdde1b22a-b1bc-4485-b435-ca1396ebfaa8/dqc_reference/reference_markers.fasta -out GCF_003851005.1_ASM385100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:44,979] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:44,983] [INFO] Selected 19 target genomes.
[2024-01-24 13:22:44,984] [INFO] Target genome list was writen to GCF_003851005.1_ASM385100v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:44,995] [INFO] Task started: fastANI
[2024-01-24 13:22:44,995] [INFO] Running command: fastANI --query /var/lib/cwl/stgbed84822-a8cf-48e8-9fa7-d1df541ce68d/GCF_003851005.1_ASM385100v1_genomic.fna.gz --refList GCF_003851005.1_ASM385100v1_genomic.fna/target_genomes.txt --output GCF_003851005.1_ASM385100v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:07,472] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:07,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdde1b22a-b1bc-4485-b435-ca1396ebfaa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:07,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdde1b22a-b1bc-4485-b435-ca1396ebfaa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:07,480] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:07,480] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:07,481] [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
Desulfonema ishimotonii	strain=Tokyo 01	GCA_003851005.1	45657	45657	type	True	100.0	2209	2209	95	conclusive
Desulfococcus multivorans	strain=DSM 2059	GCA_001854245.1	897	897	type	True	77.0146	196	2209	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_002009335.2	897	897	type	True	76.9895	194	2209	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_900167235.1	897	897	type	True	76.8156	196	2209	95	below_threshold
Desulfosarcina ovata subsp. sediminis	strain=28bB2T	GCA_009688985.1	885957	83564	type	True	76.7296	137	2209	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_000422185.1	897	897	type	True	76.6987	190	2209	95	below_threshold
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	76.6273	153	2209	95	below_threshold
Desulfosarcina alkanivorans	strain=PL12	GCA_009688945.1	571177	571177	type	True	76.5966	176	2209	95	below_threshold
Desulfatibacillum alkenivorans	strain=DSM 16219	GCA_900142135.1	259354	259354	type	True	76.4186	90	2209	95	below_threshold
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	76.2969	146	2209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:07,482] [INFO] DFAST Taxonomy check result was written to GCF_003851005.1_ASM385100v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:07,482] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:07,482] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:07,482] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdde1b22a-b1bc-4485-b435-ca1396ebfaa8/dqc_reference/checkm_data
[2024-01-24 13:23:07,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:07,545] [INFO] Task started: CheckM
[2024-01-24 13:23:07,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003851005.1_ASM385100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003851005.1_ASM385100v1_genomic.fna/checkm_input GCF_003851005.1_ASM385100v1_genomic.fna/checkm_result
[2024-01-24 13:23:57,629] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:57,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:57,647] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:57,647] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:57,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003851005.1_ASM385100v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:57,647] [INFO] Task started: Blastn
[2024-01-24 13:23:57,648] [INFO] Running command: blastn -query GCF_003851005.1_ASM385100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdde1b22a-b1bc-4485-b435-ca1396ebfaa8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003851005.1_ASM385100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:58,600] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:58,603] [INFO] Selected 22 target genomes.
[2024-01-24 13:23:58,603] [INFO] Target genome list was writen to GCF_003851005.1_ASM385100v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:58,615] [INFO] Task started: fastANI
[2024-01-24 13:23:58,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgbed84822-a8cf-48e8-9fa7-d1df541ce68d/GCF_003851005.1_ASM385100v1_genomic.fna.gz --refList GCF_003851005.1_ASM385100v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003851005.1_ASM385100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:21,813] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:21,820] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:21,821] [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_003851005.1	s__Desulfonema_B ishimotonii	100.0	2208	2209	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__Desulfonema_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001854245.1	s__Desulfococcus multivorans	77.0241	195	2209	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__Desulfococcus	95.0	100.00	99.99	1.00	1.00	4	-
GCA_011390315.1	s__JAABSQ01 sp011390315	76.7598	197	2209	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABSQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390035.1	s__JAABTE01 sp011390035	76.6094	102	2209	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389855.1	s__JAABTD01 sp011389855	76.5791	174	2209	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390065.1	s__JAABTD01 sp011390065	76.4788	172	2209	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142135.1	s__Desulfatibacillum alkenivorans	76.4186	90	2209	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfatibacillaceae;g__Desulfatibacillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390345.1	s__JAABSP01 sp011390345	76.4145	175	2209	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABSP01	95.0	95.08	95.08	0.82	0.82	2	-
GCF_009689005.1	s__Desulfosarcina ovata	76.2519	145	2209	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	97.03	97.03	0.77	0.77	2	-
GCA_011390755.1	s__JAABRU01 sp011390755	76.2311	235	2209	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABRU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237395.1	s__JABZFP01 sp014237395	75.7608	108	2209	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA5852;g__JABZFP01	95.0	99.49	98.98	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:21,822] [INFO] GTDB search result was written to GCF_003851005.1_ASM385100v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:21,822] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:21,825] [INFO] DFAST_QC result json was written to GCF_003851005.1_ASM385100v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:21,825] [INFO] DFAST_QC completed!
[2024-01-24 13:24:21,825] [INFO] Total running time: 0h1m56s