[2023-06-05 04:14:19,766] [INFO] DFAST_QC pipeline started.
[2023-06-05 04:14:19,772] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 04:14:19,773] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbf60e04-b84a-48db-b7f1-66b5f3932248/dqc_reference
[2023-06-05 04:14:21,153] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 04:14:21,154] [INFO] Task started: Prodigal
[2023-06-05 04:14:21,154] [INFO] Running command: gunzip -c /var/lib/cwl/stgac180010-4ec2-418b-9a5e-8615cf16f126/GCA_001830985.1_ASM183098v1_genomic.fna.gz | prodigal -d GCA_001830985.1_ASM183098v1_genomic.fna/cds.fna -a GCA_001830985.1_ASM183098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:14:27,055] [INFO] Task succeeded: Prodigal
[2023-06-05 04:14:27,055] [INFO] Task started: HMMsearch
[2023-06-05 04:14:27,055] [INFO] Running command: hmmsearch --tblout GCA_001830985.1_ASM183098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbf60e04-b84a-48db-b7f1-66b5f3932248/dqc_reference/reference_markers.hmm GCA_001830985.1_ASM183098v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:14:27,341] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:14:27,342] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgac180010-4ec2-418b-9a5e-8615cf16f126/GCA_001830985.1_ASM183098v1_genomic.fna.gz]
[2023-06-05 04:14:27,375] [INFO] Query marker FASTA was written to GCA_001830985.1_ASM183098v1_genomic.fna/markers.fasta
[2023-06-05 04:14:27,375] [INFO] Task started: Blastn
[2023-06-05 04:14:27,376] [INFO] Running command: blastn -query GCA_001830985.1_ASM183098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbf60e04-b84a-48db-b7f1-66b5f3932248/dqc_reference/reference_markers.fasta -out GCA_001830985.1_ASM183098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:14:27,985] [INFO] Task succeeded: Blastn
[2023-06-05 04:14:27,989] [INFO] Selected 20 target genomes.
[2023-06-05 04:14:27,989] [INFO] Target genome list was writen to GCA_001830985.1_ASM183098v1_genomic.fna/target_genomes.txt
[2023-06-05 04:14:28,010] [INFO] Task started: fastANI
[2023-06-05 04:14:28,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgac180010-4ec2-418b-9a5e-8615cf16f126/GCA_001830985.1_ASM183098v1_genomic.fna.gz --refList GCA_001830985.1_ASM183098v1_genomic.fna/target_genomes.txt --output GCA_001830985.1_ASM183098v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:14:39,470] [INFO] Task succeeded: fastANI
[2023-06-05 04:14:39,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbf60e04-b84a-48db-b7f1-66b5f3932248/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:14:39,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbf60e04-b84a-48db-b7f1-66b5f3932248/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:14:39,473] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:14:39,473] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 04:14:39,473] [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
--------------------------------------------------------------------------------
[2023-06-05 04:14:39,475] [INFO] DFAST Taxonomy check result was written to GCA_001830985.1_ASM183098v1_genomic.fna/tc_result.tsv
[2023-06-05 04:14:39,476] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:14:39,476] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:14:39,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbf60e04-b84a-48db-b7f1-66b5f3932248/dqc_reference/checkm_data
[2023-06-05 04:14:39,479] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:14:39,511] [INFO] Task started: CheckM
[2023-06-05 04:14:39,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001830985.1_ASM183098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001830985.1_ASM183098v1_genomic.fna/checkm_input GCA_001830985.1_ASM183098v1_genomic.fna/checkm_result
[2023-06-05 04:15:03,676] [INFO] Task succeeded: CheckM
[2023-06-05 04:15:03,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.98%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 04:15:03,698] [INFO] ===== Completeness check finished =====
[2023-06-05 04:15:03,699] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:15:03,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001830985.1_ASM183098v1_genomic.fna/markers.fasta)
[2023-06-05 04:15:03,699] [INFO] Task started: Blastn
[2023-06-05 04:15:03,699] [INFO] Running command: blastn -query GCA_001830985.1_ASM183098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbf60e04-b84a-48db-b7f1-66b5f3932248/dqc_reference/reference_markers_gtdb.fasta -out GCA_001830985.1_ASM183098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:15:04,634] [INFO] Task succeeded: Blastn
[2023-06-05 04:15:04,638] [INFO] Selected 22 target genomes.
[2023-06-05 04:15:04,639] [INFO] Target genome list was writen to GCA_001830985.1_ASM183098v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:15:04,938] [INFO] Task started: fastANI
[2023-06-05 04:15:04,938] [INFO] Running command: fastANI --query /var/lib/cwl/stgac180010-4ec2-418b-9a5e-8615cf16f126/GCA_001830985.1_ASM183098v1_genomic.fna.gz --refList GCA_001830985.1_ASM183098v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001830985.1_ASM183098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:15:12,849] [INFO] Task succeeded: fastANI
[2023-06-05 04:15:12,859] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 04:15:12,860] [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_002780895.1	s__0-14-3-00-41-53 sp002780895	81.4136	324	908	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__SM23-35;g__0-14-3-00-41-53	95.0	99.87	99.75	0.91	0.85	7	-
GCA_001805125.1	s__RBG-13-39-12 sp001805125	78.0583	248	908	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__SM23-35;g__RBG-13-39-12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212245.1	s__JACRGU01 sp016212245	78.0043	150	908	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__SM23-35;g__JACRGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873595.1	s__VGWZ01 sp016873595	77.4914	144	908	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__SM23-35;g__VGWZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873575.1	s__VGWY01 sp016873575	77.215	134	908	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__SM23-35;g__VGWY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328665.1	s__UBA2194 sp002328665	75.9263	97	908	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__SM23-35;g__UBA2194	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 04:15:12,862] [INFO] GTDB search result was written to GCA_001830985.1_ASM183098v1_genomic.fna/result_gtdb.tsv
[2023-06-05 04:15:12,862] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:15:12,865] [INFO] DFAST_QC result json was written to GCA_001830985.1_ASM183098v1_genomic.fna/dqc_result.json
[2023-06-05 04:15:12,865] [INFO] DFAST_QC completed!
[2023-06-05 04:15:12,865] [INFO] Total running time: 0h0m53s