[2023-03-16 18:07:32,493] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:07:32,494] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:07:32,494] [INFO] DQC Reference Directory: /var/lib/cwl/stg5820189a-865f-403b-bd83-77740b58da37/dqc_reference
[2023-03-16 18:07:35,533] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:07:35,549] [INFO] Task started: Prodigal
[2023-03-16 18:07:35,550] [INFO] Running command: cat /var/lib/cwl/stg55d0c8cf-0c57-4f9e-ae44-d8d006a522e3/OceanDNA-b20726.fa | prodigal -d OceanDNA-b20726/cds.fna -a OceanDNA-b20726/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:07:41,678] [INFO] Task succeeded: Prodigal
[2023-03-16 18:07:41,679] [INFO] Task started: HMMsearch
[2023-03-16 18:07:41,679] [INFO] Running command: hmmsearch --tblout OceanDNA-b20726/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5820189a-865f-403b-bd83-77740b58da37/dqc_reference/reference_markers.hmm OceanDNA-b20726/protein.faa > /dev/null
[2023-03-16 18:07:41,920] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:07:41,921] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg55d0c8cf-0c57-4f9e-ae44-d8d006a522e3/OceanDNA-b20726.fa]
[2023-03-16 18:07:41,929] [INFO] Query marker FASTA was written to OceanDNA-b20726/markers.fasta
[2023-03-16 18:07:41,931] [INFO] Task started: Blastn
[2023-03-16 18:07:41,931] [INFO] Running command: blastn -query OceanDNA-b20726/markers.fasta -db /var/lib/cwl/stg5820189a-865f-403b-bd83-77740b58da37/dqc_reference/reference_markers.fasta -out OceanDNA-b20726/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:07:42,514] [INFO] Task succeeded: Blastn
[2023-03-16 18:07:42,515] [INFO] Selected 6 target genomes.
[2023-03-16 18:07:42,515] [INFO] Target genome list was writen to OceanDNA-b20726/target_genomes.txt
[2023-03-16 18:07:42,522] [INFO] Task started: fastANI
[2023-03-16 18:07:42,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg55d0c8cf-0c57-4f9e-ae44-d8d006a522e3/OceanDNA-b20726.fa --refList OceanDNA-b20726/target_genomes.txt --output OceanDNA-b20726/fastani_result.tsv --threads 1
[2023-03-16 18:07:45,867] [INFO] Task succeeded: fastANI
[2023-03-16 18:07:45,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5820189a-865f-403b-bd83-77740b58da37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:07:45,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5820189a-865f-403b-bd83-77740b58da37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:07:45,868] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:07:45,868] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:07:45,869] [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
--------------------------------------------------------------------------------
[2023-03-16 18:07:45,869] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20726/tc_result.tsv
[2023-03-16 18:07:45,869] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:07:45,869] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:07:45,869] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5820189a-865f-403b-bd83-77740b58da37/dqc_reference/checkm_data
[2023-03-16 18:07:45,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:07:45,926] [INFO] Task started: CheckM
[2023-03-16 18:07:45,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20726/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20726/checkm_input OceanDNA-b20726/checkm_result
[2023-03-16 18:08:04,448] [INFO] Task succeeded: CheckM
[2023-03-16 18:08:04,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.29%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 18:08:04,451] [INFO] ===== Completeness check finished =====
[2023-03-16 18:08:04,451] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:08:04,451] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20726/markers.fasta)
[2023-03-16 18:08:04,453] [INFO] Task started: Blastn
[2023-03-16 18:08:04,453] [INFO] Running command: blastn -query OceanDNA-b20726/markers.fasta -db /var/lib/cwl/stg5820189a-865f-403b-bd83-77740b58da37/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20726/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:08:05,273] [INFO] Task succeeded: Blastn
[2023-03-16 18:08:05,274] [INFO] Selected 14 target genomes.
[2023-03-16 18:08:05,274] [INFO] Target genome list was writen to OceanDNA-b20726/target_genomes_gtdb.txt
[2023-03-16 18:08:05,289] [INFO] Task started: fastANI
[2023-03-16 18:08:05,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg55d0c8cf-0c57-4f9e-ae44-d8d006a522e3/OceanDNA-b20726.fa --refList OceanDNA-b20726/target_genomes_gtdb.txt --output OceanDNA-b20726/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:08:09,144] [INFO] Task succeeded: fastANI
[2023-03-16 18:08:09,148] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:08:09,148] [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_014239355.1	s__TMED6 sp014239355	83.1199	227	294	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710085.1	s__TMED6 sp002710085	82.8029	121	294	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167465.1	s__TMED6 sp002167465	79.492	197	294	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	98.36	98.36	0.95	0.95	2	-
GCA_002701185.1	s__TMED6 sp002701185	78.1742	130	294	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711465.1	s__TMED6 sp002711465	78.086	134	294	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:08:09,149] [INFO] GTDB search result was written to OceanDNA-b20726/result_gtdb.tsv
[2023-03-16 18:08:09,149] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:08:09,150] [INFO] DFAST_QC result json was written to OceanDNA-b20726/dqc_result.json
[2023-03-16 18:08:09,150] [INFO] DFAST_QC completed!
[2023-03-16 18:08:09,150] [INFO] Total running time: 0h0m37s