[2023-03-18 00:02:09,264] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:02:09,264] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:02:09,264] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bf6dd87-6341-4eeb-878b-2f47819a66c9/dqc_reference
[2023-03-18 00:02:10,395] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:02:10,395] [INFO] Task started: Prodigal
[2023-03-18 00:02:10,395] [INFO] Running command: cat /var/lib/cwl/stg63d597fd-ade7-462e-bbfa-c11998ca2cc4/OceanDNA-b10888.fa | prodigal -d OceanDNA-b10888/cds.fna -a OceanDNA-b10888/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:02:19,590] [INFO] Task succeeded: Prodigal
[2023-03-18 00:02:19,591] [INFO] Task started: HMMsearch
[2023-03-18 00:02:19,591] [INFO] Running command: hmmsearch --tblout OceanDNA-b10888/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bf6dd87-6341-4eeb-878b-2f47819a66c9/dqc_reference/reference_markers.hmm OceanDNA-b10888/protein.faa > /dev/null
[2023-03-18 00:02:19,747] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:02:19,748] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg63d597fd-ade7-462e-bbfa-c11998ca2cc4/OceanDNA-b10888.fa]
[2023-03-18 00:02:19,759] [INFO] Query marker FASTA was written to OceanDNA-b10888/markers.fasta
[2023-03-18 00:02:19,760] [INFO] Task started: Blastn
[2023-03-18 00:02:19,761] [INFO] Running command: blastn -query OceanDNA-b10888/markers.fasta -db /var/lib/cwl/stg8bf6dd87-6341-4eeb-878b-2f47819a66c9/dqc_reference/reference_markers.fasta -out OceanDNA-b10888/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:02:20,356] [INFO] Task succeeded: Blastn
[2023-03-18 00:02:20,357] [INFO] Selected 28 target genomes.
[2023-03-18 00:02:20,358] [INFO] Target genome list was writen to OceanDNA-b10888/target_genomes.txt
[2023-03-18 00:02:20,375] [INFO] Task started: fastANI
[2023-03-18 00:02:20,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg63d597fd-ade7-462e-bbfa-c11998ca2cc4/OceanDNA-b10888.fa --refList OceanDNA-b10888/target_genomes.txt --output OceanDNA-b10888/fastani_result.tsv --threads 1
[2023-03-18 00:02:38,192] [INFO] Task succeeded: fastANI
[2023-03-18 00:02:38,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bf6dd87-6341-4eeb-878b-2f47819a66c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:02:38,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bf6dd87-6341-4eeb-878b-2f47819a66c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:02:38,193] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:02:38,193] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:02:38,193] [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 00:02:38,193] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10888/tc_result.tsv
[2023-03-18 00:02:38,193] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:02:38,193] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:02:38,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bf6dd87-6341-4eeb-878b-2f47819a66c9/dqc_reference/checkm_data
[2023-03-18 00:02:38,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:02:38,432] [INFO] Task started: CheckM
[2023-03-18 00:02:38,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10888/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10888/checkm_input OceanDNA-b10888/checkm_result
[2023-03-18 00:03:06,508] [INFO] Task succeeded: CheckM
[2023-03-18 00:03:06,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:03:06,510] [INFO] ===== Completeness check finished =====
[2023-03-18 00:03:06,511] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:03:06,511] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10888/markers.fasta)
[2023-03-18 00:03:06,512] [INFO] Task started: Blastn
[2023-03-18 00:03:06,512] [INFO] Running command: blastn -query OceanDNA-b10888/markers.fasta -db /var/lib/cwl/stg8bf6dd87-6341-4eeb-878b-2f47819a66c9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10888/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:03:07,425] [INFO] Task succeeded: Blastn
[2023-03-18 00:03:07,426] [INFO] Selected 15 target genomes.
[2023-03-18 00:03:07,426] [INFO] Target genome list was writen to OceanDNA-b10888/target_genomes_gtdb.txt
[2023-03-18 00:03:07,498] [INFO] Task started: fastANI
[2023-03-18 00:03:07,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg63d597fd-ade7-462e-bbfa-c11998ca2cc4/OceanDNA-b10888.fa --refList OceanDNA-b10888/target_genomes_gtdb.txt --output OceanDNA-b10888/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:03:13,437] [INFO] Task succeeded: fastANI
[2023-03-18 00:03:13,442] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:03:13,442] [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_905181615.1	s__UBA7428 sp905181615	79.1707	279	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
GCA_003023645.1	s__UBA7428 sp003023645	78.5815	198	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.50	99.50	0.87	0.87	2	-
GCA_018608425.1	s__UBA7428 sp018608425	78.5794	142	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477625.1	s__UBA7428 sp002477625	78.3952	140	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.28	97.25	0.74	0.68	4	-
GCA_002708445.1	s__UBA7428 sp002708445	77.6281	129	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182305.1	s__MS024-2A sp905182305	76.2122	57	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:03:13,442] [INFO] GTDB search result was written to OceanDNA-b10888/result_gtdb.tsv
[2023-03-18 00:03:13,442] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:03:13,443] [INFO] DFAST_QC result json was written to OceanDNA-b10888/dqc_result.json
[2023-03-18 00:03:13,443] [INFO] DFAST_QC completed!
[2023-03-18 00:03:13,443] [INFO] Total running time: 0h1m4s