[2023-03-18 04:39:40,267] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:39:40,267] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:39:40,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg2be9d9dc-1f42-4e76-9995-3eb01412dc90/dqc_reference
[2023-03-18 04:39:41,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:39:41,379] [INFO] Task started: Prodigal
[2023-03-18 04:39:41,379] [INFO] Running command: cat /var/lib/cwl/stgce1587fe-19b1-4c68-bf4c-b19da30272ba/OceanDNA-b20668.fa | prodigal -d OceanDNA-b20668/cds.fna -a OceanDNA-b20668/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:39:48,357] [INFO] Task succeeded: Prodigal
[2023-03-18 04:39:48,357] [INFO] Task started: HMMsearch
[2023-03-18 04:39:48,357] [INFO] Running command: hmmsearch --tblout OceanDNA-b20668/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2be9d9dc-1f42-4e76-9995-3eb01412dc90/dqc_reference/reference_markers.hmm OceanDNA-b20668/protein.faa > /dev/null
[2023-03-18 04:39:48,524] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:39:48,524] [INFO] Found 6/6 markers.
[2023-03-18 04:39:48,535] [INFO] Query marker FASTA was written to OceanDNA-b20668/markers.fasta
[2023-03-18 04:39:48,535] [INFO] Task started: Blastn
[2023-03-18 04:39:48,535] [INFO] Running command: blastn -query OceanDNA-b20668/markers.fasta -db /var/lib/cwl/stg2be9d9dc-1f42-4e76-9995-3eb01412dc90/dqc_reference/reference_markers.fasta -out OceanDNA-b20668/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:39:49,052] [INFO] Task succeeded: Blastn
[2023-03-18 04:39:49,053] [INFO] Selected 15 target genomes.
[2023-03-18 04:39:49,053] [INFO] Target genome list was writen to OceanDNA-b20668/target_genomes.txt
[2023-03-18 04:39:49,060] [INFO] Task started: fastANI
[2023-03-18 04:39:49,060] [INFO] Running command: fastANI --query /var/lib/cwl/stgce1587fe-19b1-4c68-bf4c-b19da30272ba/OceanDNA-b20668.fa --refList OceanDNA-b20668/target_genomes.txt --output OceanDNA-b20668/fastani_result.tsv --threads 1
[2023-03-18 04:39:55,049] [INFO] Task succeeded: fastANI
[2023-03-18 04:39:55,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2be9d9dc-1f42-4e76-9995-3eb01412dc90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:39:55,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2be9d9dc-1f42-4e76-9995-3eb01412dc90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:39:55,050] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:39:55,050] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:39:55,050] [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
--------------------------------------------------------------------------------
[2023-03-18 04:39:55,050] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20668/tc_result.tsv
[2023-03-18 04:39:55,050] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:39:55,050] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:39:55,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2be9d9dc-1f42-4e76-9995-3eb01412dc90/dqc_reference/checkm_data
[2023-03-18 04:39:55,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:39:55,056] [INFO] Task started: CheckM
[2023-03-18 04:39:55,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20668/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20668/checkm_input OceanDNA-b20668/checkm_result
[2023-03-18 04:40:17,409] [INFO] Task succeeded: CheckM
[2023-03-18 04:40:17,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:40:17,411] [INFO] ===== Completeness check finished =====
[2023-03-18 04:40:17,411] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:40:17,411] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20668/markers.fasta)
[2023-03-18 04:40:17,411] [INFO] Task started: Blastn
[2023-03-18 04:40:17,411] [INFO] Running command: blastn -query OceanDNA-b20668/markers.fasta -db /var/lib/cwl/stg2be9d9dc-1f42-4e76-9995-3eb01412dc90/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20668/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:40:18,165] [INFO] Task succeeded: Blastn
[2023-03-18 04:40:18,166] [INFO] Selected 23 target genomes.
[2023-03-18 04:40:18,166] [INFO] Target genome list was writen to OceanDNA-b20668/target_genomes_gtdb.txt
[2023-03-18 04:40:18,192] [INFO] Task started: fastANI
[2023-03-18 04:40:18,193] [INFO] Running command: fastANI --query /var/lib/cwl/stgce1587fe-19b1-4c68-bf4c-b19da30272ba/OceanDNA-b20668.fa --refList OceanDNA-b20668/target_genomes_gtdb.txt --output OceanDNA-b20668/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:40:24,324] [INFO] Task succeeded: fastANI
[2023-03-18 04:40:24,327] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:40:24,327] [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_002703645.1	s__TMED161 sp002703645	94.0795	375	471	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED161;g__TMED161	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731795.1	s__TMED161 sp002731795	76.8145	87	471	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED161;g__TMED161	95.0	98.59	98.59	0.77	0.77	2	-
GCA_002171125.1	s__TMED161 sp002171125	76.7216	86	471	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED161;g__TMED161	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:40:24,328] [INFO] GTDB search result was written to OceanDNA-b20668/result_gtdb.tsv
[2023-03-18 04:40:24,328] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:40:24,328] [INFO] DFAST_QC result json was written to OceanDNA-b20668/dqc_result.json
[2023-03-18 04:40:24,328] [INFO] DFAST_QC completed!
[2023-03-18 04:40:24,328] [INFO] Total running time: 0h0m44s