[2023-03-19 00:43:03,144] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:43:03,144] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:43:03,144] [INFO] DQC Reference Directory: /var/lib/cwl/stg8be68894-b644-4c37-9492-bfe474fc67e1/dqc_reference
[2023-03-19 00:43:04,288] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:43:04,289] [INFO] Task started: Prodigal
[2023-03-19 00:43:04,290] [INFO] Running command: cat /var/lib/cwl/stg5f572bcb-cb06-431b-94bc-971328374e39/OceanDNA-b8901.fa | prodigal -d OceanDNA-b8901/cds.fna -a OceanDNA-b8901/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:43:08,090] [INFO] Task succeeded: Prodigal
[2023-03-19 00:43:08,091] [INFO] Task started: HMMsearch
[2023-03-19 00:43:08,091] [INFO] Running command: hmmsearch --tblout OceanDNA-b8901/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8be68894-b644-4c37-9492-bfe474fc67e1/dqc_reference/reference_markers.hmm OceanDNA-b8901/protein.faa > /dev/null
[2023-03-19 00:43:08,264] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:43:08,265] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5f572bcb-cb06-431b-94bc-971328374e39/OceanDNA-b8901.fa]
[2023-03-19 00:43:08,281] [INFO] Query marker FASTA was written to OceanDNA-b8901/markers.fasta
[2023-03-19 00:43:08,283] [INFO] Task started: Blastn
[2023-03-19 00:43:08,283] [INFO] Running command: blastn -query OceanDNA-b8901/markers.fasta -db /var/lib/cwl/stg8be68894-b644-4c37-9492-bfe474fc67e1/dqc_reference/reference_markers.fasta -out OceanDNA-b8901/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:43:08,849] [INFO] Task succeeded: Blastn
[2023-03-19 00:43:08,854] [INFO] Selected 30 target genomes.
[2023-03-19 00:43:08,854] [INFO] Target genome list was writen to OceanDNA-b8901/target_genomes.txt
[2023-03-19 00:43:08,874] [INFO] Task started: fastANI
[2023-03-19 00:43:08,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f572bcb-cb06-431b-94bc-971328374e39/OceanDNA-b8901.fa --refList OceanDNA-b8901/target_genomes.txt --output OceanDNA-b8901/fastani_result.tsv --threads 1
[2023-03-19 00:43:23,381] [INFO] Task succeeded: fastANI
[2023-03-19 00:43:23,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8be68894-b644-4c37-9492-bfe474fc67e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:43:23,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8be68894-b644-4c37-9492-bfe474fc67e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:43:23,382] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:43:23,382] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:43:23,382] [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
--------------------------------------------------------------------------------
[2023-03-19 00:43:23,383] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8901/tc_result.tsv
[2023-03-19 00:43:23,383] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:43:23,383] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:43:23,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8be68894-b644-4c37-9492-bfe474fc67e1/dqc_reference/checkm_data
[2023-03-19 00:43:23,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:43:23,457] [INFO] Task started: CheckM
[2023-03-19 00:43:23,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8901/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8901/checkm_input OceanDNA-b8901/checkm_result
[2023-03-19 00:43:40,129] [INFO] Task succeeded: CheckM
[2023-03-19 00:43:40,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:43:40,144] [INFO] ===== Completeness check finished =====
[2023-03-19 00:43:40,144] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:43:40,144] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8901/markers.fasta)
[2023-03-19 00:43:40,145] [INFO] Task started: Blastn
[2023-03-19 00:43:40,145] [INFO] Running command: blastn -query OceanDNA-b8901/markers.fasta -db /var/lib/cwl/stg8be68894-b644-4c37-9492-bfe474fc67e1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8901/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:43:41,019] [INFO] Task succeeded: Blastn
[2023-03-19 00:43:41,023] [INFO] Selected 16 target genomes.
[2023-03-19 00:43:41,023] [INFO] Target genome list was writen to OceanDNA-b8901/target_genomes_gtdb.txt
[2023-03-19 00:43:41,032] [INFO] Task started: fastANI
[2023-03-19 00:43:41,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f572bcb-cb06-431b-94bc-971328374e39/OceanDNA-b8901.fa --refList OceanDNA-b8901/target_genomes_gtdb.txt --output OceanDNA-b8901/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:43:44,297] [INFO] Task succeeded: fastANI
[2023-03-19 00:43:44,302] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:43:44,302] [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_902587325.1	s__MED-G14 sp902587325	82.8636	110	136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	97.53	95.17	0.82	0.78	10	-
GCA_002457715.1	s__MED-G14 sp002457715	80.0358	81	136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	98.34	98.31	0.91	0.89	3	-
GCA_002693085.1	s__MED-G14 sp002693085	79.8513	62	136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520835.1	s__MED-G14 sp902520835	79.6237	92	136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702385.1	s__MED-G14 sp002702385	79.4587	67	136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902554655.1	s__MED-G14 sp902554655	79.0012	75	136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	99.59	99.59	0.62	0.62	2	-
--------------------------------------------------------------------------------
[2023-03-19 00:43:44,304] [INFO] GTDB search result was written to OceanDNA-b8901/result_gtdb.tsv
[2023-03-19 00:43:44,307] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:43:44,310] [INFO] DFAST_QC result json was written to OceanDNA-b8901/dqc_result.json
[2023-03-19 00:43:44,310] [INFO] DFAST_QC completed!
[2023-03-19 00:43:44,310] [INFO] Total running time: 0h0m41s