[2023-06-18 23:17:32,919] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:17:32,922] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:17:32,923] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc9ec14d-b41d-4765-9a7a-e006daea66b9/dqc_reference
[2023-06-18 23:17:34,312] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:17:34,313] [INFO] Task started: Prodigal
[2023-06-18 23:17:34,313] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8d34e4a-291e-42cb-8ce1-51a974a63c1e/GCA_013202495.1_ASM1320249v1_genomic.fna.gz | prodigal -d GCA_013202495.1_ASM1320249v1_genomic.fna/cds.fna -a GCA_013202495.1_ASM1320249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:17:43,039] [INFO] Task succeeded: Prodigal
[2023-06-18 23:17:43,040] [INFO] Task started: HMMsearch
[2023-06-18 23:17:43,040] [INFO] Running command: hmmsearch --tblout GCA_013202495.1_ASM1320249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc9ec14d-b41d-4765-9a7a-e006daea66b9/dqc_reference/reference_markers.hmm GCA_013202495.1_ASM1320249v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:17:43,310] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:17:43,311] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd8d34e4a-291e-42cb-8ce1-51a974a63c1e/GCA_013202495.1_ASM1320249v1_genomic.fna.gz]
[2023-06-18 23:17:43,354] [INFO] Query marker FASTA was written to GCA_013202495.1_ASM1320249v1_genomic.fna/markers.fasta
[2023-06-18 23:17:43,355] [INFO] Task started: Blastn
[2023-06-18 23:17:43,355] [INFO] Running command: blastn -query GCA_013202495.1_ASM1320249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc9ec14d-b41d-4765-9a7a-e006daea66b9/dqc_reference/reference_markers.fasta -out GCA_013202495.1_ASM1320249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:17:43,961] [INFO] Task succeeded: Blastn
[2023-06-18 23:17:43,965] [INFO] Selected 9 target genomes.
[2023-06-18 23:17:43,966] [INFO] Target genome list was writen to GCA_013202495.1_ASM1320249v1_genomic.fna/target_genomes.txt
[2023-06-18 23:17:43,967] [INFO] Task started: fastANI
[2023-06-18 23:17:43,967] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8d34e4a-291e-42cb-8ce1-51a974a63c1e/GCA_013202495.1_ASM1320249v1_genomic.fna.gz --refList GCA_013202495.1_ASM1320249v1_genomic.fna/target_genomes.txt --output GCA_013202495.1_ASM1320249v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:17:51,211] [INFO] Task succeeded: fastANI
[2023-06-18 23:17:51,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc9ec14d-b41d-4765-9a7a-e006daea66b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:17:51,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc9ec14d-b41d-4765-9a7a-e006daea66b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:17:51,214] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 23:17:51,214] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 23:17:51,214] [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
--------------------------------------------------------------------------------
[2023-06-18 23:17:51,217] [INFO] DFAST Taxonomy check result was written to GCA_013202495.1_ASM1320249v1_genomic.fna/tc_result.tsv
[2023-06-18 23:17:51,218] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:17:51,218] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:17:51,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc9ec14d-b41d-4765-9a7a-e006daea66b9/dqc_reference/checkm_data
[2023-06-18 23:17:51,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:17:51,278] [INFO] Task started: CheckM
[2023-06-18 23:17:51,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013202495.1_ASM1320249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013202495.1_ASM1320249v1_genomic.fna/checkm_input GCA_013202495.1_ASM1320249v1_genomic.fna/checkm_result
[2023-06-18 23:18:24,691] [INFO] Task succeeded: CheckM
[2023-06-18 23:18:24,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 23:18:24,713] [INFO] ===== Completeness check finished =====
[2023-06-18 23:18:24,713] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:18:24,713] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013202495.1_ASM1320249v1_genomic.fna/markers.fasta)
[2023-06-18 23:18:24,714] [INFO] Task started: Blastn
[2023-06-18 23:18:24,714] [INFO] Running command: blastn -query GCA_013202495.1_ASM1320249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc9ec14d-b41d-4765-9a7a-e006daea66b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_013202495.1_ASM1320249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:18:25,497] [INFO] Task succeeded: Blastn
[2023-06-18 23:18:25,502] [INFO] Selected 7 target genomes.
[2023-06-18 23:18:25,502] [INFO] Target genome list was writen to GCA_013202495.1_ASM1320249v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:18:25,503] [INFO] Task started: fastANI
[2023-06-18 23:18:25,503] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8d34e4a-291e-42cb-8ce1-51a974a63c1e/GCA_013202495.1_ASM1320249v1_genomic.fna.gz --refList GCA_013202495.1_ASM1320249v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013202495.1_ASM1320249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:18:31,365] [INFO] Task succeeded: fastANI
[2023-06-18 23:18:31,380] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 23:18:31,380] [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_013202495.1	s__JABMPR01 sp013202495	100.0	1180	1190	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016784025.1	s__JABMPR01 sp014382565	90.8357	824	1190	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.96	99.93	0.94	0.93	3	-
GCA_018650445.1	s__JABMPR01 sp018650445	86.5735	662	1190	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.76	99.61	0.86	0.82	5	-
GCA_018673925.1	s__JABMPR01 sp018673925	85.8691	760	1190	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.95	99.91	0.96	0.94	16	-
GCA_016784545.1	s__JABMPR01 sp016784545	82.9483	680	1190	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018650795.1	s__JABMPR01 sp018650795	80.4803	524	1190	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.79	99.56	0.89	0.81	14	-
GCA_013203185.1	s__JABMPR01 sp013203185	80.2524	539	1190	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 23:18:31,383] [INFO] GTDB search result was written to GCA_013202495.1_ASM1320249v1_genomic.fna/result_gtdb.tsv
[2023-06-18 23:18:31,383] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:18:31,387] [INFO] DFAST_QC result json was written to GCA_013202495.1_ASM1320249v1_genomic.fna/dqc_result.json
[2023-06-18 23:18:31,387] [INFO] DFAST_QC completed!
[2023-06-18 23:18:31,388] [INFO] Total running time: 0h0m58s