[2023-06-04 22:52:04,537] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:52:04,541] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:52:04,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c49c2ae-6450-4541-b21e-f9b1c55bab6e/dqc_reference
[2023-06-04 22:52:06,791] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:52:06,792] [INFO] Task started: Prodigal
[2023-06-04 22:52:06,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f87502c-7be7-453a-906f-1ff970707fad/GCA_934486495.1_ERR7745994_bin.14_genomic.fna.gz | prodigal -d GCA_934486495.1_ERR7745994_bin.14_genomic.fna/cds.fna -a GCA_934486495.1_ERR7745994_bin.14_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:52:11,734] [INFO] Task succeeded: Prodigal
[2023-06-04 22:52:11,735] [INFO] Task started: HMMsearch
[2023-06-04 22:52:11,735] [INFO] Running command: hmmsearch --tblout GCA_934486495.1_ERR7745994_bin.14_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c49c2ae-6450-4541-b21e-f9b1c55bab6e/dqc_reference/reference_markers.hmm GCA_934486495.1_ERR7745994_bin.14_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:52:11,971] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:52:11,973] [INFO] Found 6/6 markers.
[2023-06-04 22:52:12,012] [INFO] Query marker FASTA was written to GCA_934486495.1_ERR7745994_bin.14_genomic.fna/markers.fasta
[2023-06-04 22:52:12,013] [INFO] Task started: Blastn
[2023-06-04 22:52:12,013] [INFO] Running command: blastn -query GCA_934486495.1_ERR7745994_bin.14_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c49c2ae-6450-4541-b21e-f9b1c55bab6e/dqc_reference/reference_markers.fasta -out GCA_934486495.1_ERR7745994_bin.14_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:52:12,640] [INFO] Task succeeded: Blastn
[2023-06-04 22:52:12,645] [INFO] Selected 28 target genomes.
[2023-06-04 22:52:12,645] [INFO] Target genome list was writen to GCA_934486495.1_ERR7745994_bin.14_genomic.fna/target_genomes.txt
[2023-06-04 22:52:12,672] [INFO] Task started: fastANI
[2023-06-04 22:52:12,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f87502c-7be7-453a-906f-1ff970707fad/GCA_934486495.1_ERR7745994_bin.14_genomic.fna.gz --refList GCA_934486495.1_ERR7745994_bin.14_genomic.fna/target_genomes.txt --output GCA_934486495.1_ERR7745994_bin.14_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:52:25,547] [INFO] Task succeeded: fastANI
[2023-06-04 22:52:25,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c49c2ae-6450-4541-b21e-f9b1c55bab6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:52:25,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c49c2ae-6450-4541-b21e-f9b1c55bab6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:52:25,550] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 22:52:25,550] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 22:52:25,551] [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
--------------------------------------------------------------------------------
[2023-06-04 22:52:25,553] [INFO] DFAST Taxonomy check result was written to GCA_934486495.1_ERR7745994_bin.14_genomic.fna/tc_result.tsv
[2023-06-04 22:52:25,554] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:52:25,554] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:52:25,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c49c2ae-6450-4541-b21e-f9b1c55bab6e/dqc_reference/checkm_data
[2023-06-04 22:52:25,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:52:25,587] [INFO] Task started: CheckM
[2023-06-04 22:52:25,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934486495.1_ERR7745994_bin.14_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934486495.1_ERR7745994_bin.14_genomic.fna/checkm_input GCA_934486495.1_ERR7745994_bin.14_genomic.fna/checkm_result
[2023-06-04 22:52:47,350] [INFO] Task succeeded: CheckM
[2023-06-04 22:52:47,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 22:52:47,379] [INFO] ===== Completeness check finished =====
[2023-06-04 22:52:47,379] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:52:47,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934486495.1_ERR7745994_bin.14_genomic.fna/markers.fasta)
[2023-06-04 22:52:47,380] [INFO] Task started: Blastn
[2023-06-04 22:52:47,380] [INFO] Running command: blastn -query GCA_934486495.1_ERR7745994_bin.14_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c49c2ae-6450-4541-b21e-f9b1c55bab6e/dqc_reference/reference_markers_gtdb.fasta -out GCA_934486495.1_ERR7745994_bin.14_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:52:48,407] [INFO] Task succeeded: Blastn
[2023-06-04 22:52:48,412] [INFO] Selected 33 target genomes.
[2023-06-04 22:52:48,412] [INFO] Target genome list was writen to GCA_934486495.1_ERR7745994_bin.14_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:52:48,479] [INFO] Task started: fastANI
[2023-06-04 22:52:48,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f87502c-7be7-453a-906f-1ff970707fad/GCA_934486495.1_ERR7745994_bin.14_genomic.fna.gz --refList GCA_934486495.1_ERR7745994_bin.14_genomic.fna/target_genomes_gtdb.txt --output GCA_934486495.1_ERR7745994_bin.14_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:52:59,871] [INFO] Task succeeded: fastANI
[2023-06-04 22:52:59,881] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 22:52:59,882] [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_905199755.1	s__UBA4716 sp905199755	78.2529	91	719	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__UBA4716	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935675.1	s__RGIG9115 sp017935675	77.1889	112	719	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__RGIG9115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002438865.1	s__UBA4716 sp002438865	76.5425	53	719	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__UBA4716	95.0	99.40	99.40	0.75	0.75	2	-
GCA_003460745.1	s__CAG-41 sp900066215	76.3773	77	719	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	97.67	97.16	0.82	0.77	17	-
--------------------------------------------------------------------------------
[2023-06-04 22:52:59,885] [INFO] GTDB search result was written to GCA_934486495.1_ERR7745994_bin.14_genomic.fna/result_gtdb.tsv
[2023-06-04 22:52:59,886] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:52:59,889] [INFO] DFAST_QC result json was written to GCA_934486495.1_ERR7745994_bin.14_genomic.fna/dqc_result.json
[2023-06-04 22:52:59,890] [INFO] DFAST_QC completed!
[2023-06-04 22:52:59,890] [INFO] Total running time: 0h0m55s