[2023-03-15 11:54:50,863] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:54:50,863] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:54:50,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d7f856f-73e0-4d5b-820b-94b17a8ca059/dqc_reference
[2023-03-15 11:54:51,974] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:54:51,975] [INFO] Task started: Prodigal
[2023-03-15 11:54:51,975] [INFO] Running command: cat /var/lib/cwl/stg4d858464-5314-4d72-816d-68e0f638e25a/OceanDNA-b14810.fa | prodigal -d OceanDNA-b14810/cds.fna -a OceanDNA-b14810/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:54:58,701] [INFO] Task succeeded: Prodigal
[2023-03-15 11:54:58,702] [INFO] Task started: HMMsearch
[2023-03-15 11:54:58,702] [INFO] Running command: hmmsearch --tblout OceanDNA-b14810/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d7f856f-73e0-4d5b-820b-94b17a8ca059/dqc_reference/reference_markers.hmm OceanDNA-b14810/protein.faa > /dev/null
[2023-03-15 11:54:58,868] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:54:58,869] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4d858464-5314-4d72-816d-68e0f638e25a/OceanDNA-b14810.fa]
[2023-03-15 11:54:58,880] [INFO] Query marker FASTA was written to OceanDNA-b14810/markers.fasta
[2023-03-15 11:54:58,881] [INFO] Task started: Blastn
[2023-03-15 11:54:58,881] [INFO] Running command: blastn -query OceanDNA-b14810/markers.fasta -db /var/lib/cwl/stg6d7f856f-73e0-4d5b-820b-94b17a8ca059/dqc_reference/reference_markers.fasta -out OceanDNA-b14810/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:54:59,386] [INFO] Task succeeded: Blastn
[2023-03-15 11:54:59,388] [INFO] Selected 17 target genomes.
[2023-03-15 11:54:59,388] [INFO] Target genome list was writen to OceanDNA-b14810/target_genomes.txt
[2023-03-15 11:54:59,398] [INFO] Task started: fastANI
[2023-03-15 11:54:59,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d858464-5314-4d72-816d-68e0f638e25a/OceanDNA-b14810.fa --refList OceanDNA-b14810/target_genomes.txt --output OceanDNA-b14810/fastani_result.tsv --threads 1
[2023-03-15 11:55:07,177] [INFO] Task succeeded: fastANI
[2023-03-15 11:55:07,177] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d7f856f-73e0-4d5b-820b-94b17a8ca059/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:55:07,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d7f856f-73e0-4d5b-820b-94b17a8ca059/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:55:07,177] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:55:07,178] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:55:07,178] [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
--------------------------------------------------------------------------------
[2023-03-15 11:55:07,179] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14810/tc_result.tsv
[2023-03-15 11:55:07,179] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:55:07,180] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:55:07,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d7f856f-73e0-4d5b-820b-94b17a8ca059/dqc_reference/checkm_data
[2023-03-15 11:55:07,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:55:07,187] [INFO] Task started: CheckM
[2023-03-15 11:55:07,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14810/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14810/checkm_input OceanDNA-b14810/checkm_result
[2023-03-15 11:55:29,250] [INFO] Task succeeded: CheckM
[2023-03-15 11:55:29,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:55:29,277] [INFO] ===== Completeness check finished =====
[2023-03-15 11:55:29,277] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:55:29,277] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14810/markers.fasta)
[2023-03-15 11:55:29,279] [INFO] Task started: Blastn
[2023-03-15 11:55:29,279] [INFO] Running command: blastn -query OceanDNA-b14810/markers.fasta -db /var/lib/cwl/stg6d7f856f-73e0-4d5b-820b-94b17a8ca059/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14810/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:55:29,992] [INFO] Task succeeded: Blastn
[2023-03-15 11:55:29,995] [INFO] Selected 15 target genomes.
[2023-03-15 11:55:29,996] [INFO] Target genome list was writen to OceanDNA-b14810/target_genomes_gtdb.txt
[2023-03-15 11:55:30,040] [INFO] Task started: fastANI
[2023-03-15 11:55:30,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d858464-5314-4d72-816d-68e0f638e25a/OceanDNA-b14810.fa --refList OceanDNA-b14810/target_genomes_gtdb.txt --output OceanDNA-b14810/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:55:33,323] [INFO] Task succeeded: fastANI
[2023-03-15 11:55:33,328] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:55:33,328] [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_002718455.1	s__GCA-2718455 sp002718455	93.3708	402	441	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-2718455	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721875.1	s__TMED-70 sp002721875	77.1503	89	441	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008373205.1	s__TMED-70 sp008373205	77.112	103	441	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	99.62	99.62	0.87	0.87	2	-
GCA_002699165.1	s__TMED-70 sp002699165	77.0748	97	441	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	99.00	98.33	0.87	0.75	4	-
GCA_002171675.1	s__TMED-70 sp002171675	76.8492	96	441	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	99.24	99.20	0.89	0.87	3	-
GCA_002719425.1	s__TMED-70 sp002719425	76.6593	83	441	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:55:33,330] [INFO] GTDB search result was written to OceanDNA-b14810/result_gtdb.tsv
[2023-03-15 11:55:33,333] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:55:33,336] [INFO] DFAST_QC result json was written to OceanDNA-b14810/dqc_result.json
[2023-03-15 11:55:33,336] [INFO] DFAST_QC completed!
[2023-03-15 11:55:33,336] [INFO] Total running time: 0h0m42s