[2023-03-15 03:56:21,762] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:56:21,762] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:56:21,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a441fae-f0d5-4791-aec6-9e6437311b80/dqc_reference
[2023-03-15 03:56:23,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:56:23,405] [INFO] Task started: Prodigal
[2023-03-15 03:56:23,405] [INFO] Running command: cat /var/lib/cwl/stg4629e8be-3dbb-4012-83f1-c72e7fedc07b/OceanDNA-b12485.fa | prodigal -d OceanDNA-b12485/cds.fna -a OceanDNA-b12485/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:56:37,641] [INFO] Task succeeded: Prodigal
[2023-03-15 03:56:37,641] [INFO] Task started: HMMsearch
[2023-03-15 03:56:37,641] [INFO] Running command: hmmsearch --tblout OceanDNA-b12485/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a441fae-f0d5-4791-aec6-9e6437311b80/dqc_reference/reference_markers.hmm OceanDNA-b12485/protein.faa > /dev/null
[2023-03-15 03:56:37,880] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:56:37,881] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4629e8be-3dbb-4012-83f1-c72e7fedc07b/OceanDNA-b12485.fa]
[2023-03-15 03:56:37,897] [INFO] Query marker FASTA was written to OceanDNA-b12485/markers.fasta
[2023-03-15 03:56:37,897] [INFO] Task started: Blastn
[2023-03-15 03:56:37,897] [INFO] Running command: blastn -query OceanDNA-b12485/markers.fasta -db /var/lib/cwl/stg2a441fae-f0d5-4791-aec6-9e6437311b80/dqc_reference/reference_markers.fasta -out OceanDNA-b12485/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:38,498] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:38,499] [INFO] Selected 20 target genomes.
[2023-03-15 03:56:38,499] [INFO] Target genome list was writen to OceanDNA-b12485/target_genomes.txt
[2023-03-15 03:56:38,508] [INFO] Task started: fastANI
[2023-03-15 03:56:38,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg4629e8be-3dbb-4012-83f1-c72e7fedc07b/OceanDNA-b12485.fa --refList OceanDNA-b12485/target_genomes.txt --output OceanDNA-b12485/fastani_result.tsv --threads 1
[2023-03-15 03:56:49,751] [INFO] Task succeeded: fastANI
[2023-03-15 03:56:49,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a441fae-f0d5-4791-aec6-9e6437311b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:56:49,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a441fae-f0d5-4791-aec6-9e6437311b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:56:49,752] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:56:49,752] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:56:49,752] [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 03:56:49,752] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12485/tc_result.tsv
[2023-03-15 03:56:49,752] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:56:49,752] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:56:49,752] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a441fae-f0d5-4791-aec6-9e6437311b80/dqc_reference/checkm_data
[2023-03-15 03:56:49,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:56:49,760] [INFO] Task started: CheckM
[2023-03-15 03:56:49,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12485/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12485/checkm_input OceanDNA-b12485/checkm_result
[2023-03-15 03:57:28,430] [INFO] Task succeeded: CheckM
[2023-03-15 03:57:28,430] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 03:57:28,433] [INFO] ===== Completeness check finished =====
[2023-03-15 03:57:28,433] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:57:28,433] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12485/markers.fasta)
[2023-03-15 03:57:28,434] [INFO] Task started: Blastn
[2023-03-15 03:57:28,434] [INFO] Running command: blastn -query OceanDNA-b12485/markers.fasta -db /var/lib/cwl/stg2a441fae-f0d5-4791-aec6-9e6437311b80/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12485/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:57:29,373] [INFO] Task succeeded: Blastn
[2023-03-15 03:57:29,374] [INFO] Selected 16 target genomes.
[2023-03-15 03:57:29,374] [INFO] Target genome list was writen to OceanDNA-b12485/target_genomes_gtdb.txt
[2023-03-15 03:57:29,390] [INFO] Task started: fastANI
[2023-03-15 03:57:29,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg4629e8be-3dbb-4012-83f1-c72e7fedc07b/OceanDNA-b12485.fa --refList OceanDNA-b12485/target_genomes_gtdb.txt --output OceanDNA-b12485/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:57:35,453] [INFO] Task succeeded: fastANI
[2023-03-15 03:57:35,460] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:57:35,460] [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_002721285.1	s__SP287 sp002721285	77.8671	144	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__SP287	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780365.1	s__MED-G20 sp016780365	76.7848	110	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	98.18	97.06	0.79	0.71	6	-
GCA_002723085.1	s__GCA-2723085 sp002723085	76.7708	119	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-2723085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182525.1	s__MED-G20 sp905182525	76.7268	131	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.07	96.07	0.86	0.86	2	-
GCA_002686655.1	s__MED-G20 sp002686655	76.6383	132	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.65	96.65	0.87	0.87	2	-
GCA_002457645.1	s__MED-G20 sp002457645	76.3656	70	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691605.1	s__MED-G20 sp002691605	76.0021	110	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.19	95.12	0.79	0.76	3	-
GCA_002716065.1	s__GCA-2716065 sp002716065	75.8948	64	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-2716065	95.0	97.60	97.60	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-15 03:57:35,460] [INFO] GTDB search result was written to OceanDNA-b12485/result_gtdb.tsv
[2023-03-15 03:57:35,461] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:57:35,461] [INFO] DFAST_QC result json was written to OceanDNA-b12485/dqc_result.json
[2023-03-15 03:57:35,462] [INFO] DFAST_QC completed!
[2023-03-15 03:57:35,462] [INFO] Total running time: 0h1m14s