[2023-03-17 00:45:47,166] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,166] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg10b354e0-26ea-4d78-92f0-f297db91364a/dqc_reference
[2023-03-17 00:45:48,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,353] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,353] [INFO] Running command: cat /var/lib/cwl/stgdac053b3-fd69-4fa8-9c18-d1aac62d7a99/OceanDNA-b46530.fa | prodigal -d OceanDNA-b46530/cds.fna -a OceanDNA-b46530/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:11,958] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:11,958] [INFO] Task started: HMMsearch
[2023-03-17 00:46:11,958] [INFO] Running command: hmmsearch --tblout OceanDNA-b46530/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10b354e0-26ea-4d78-92f0-f297db91364a/dqc_reference/reference_markers.hmm OceanDNA-b46530/protein.faa > /dev/null
[2023-03-17 00:46:12,149] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:12,150] [INFO] Found 6/6 markers.
[2023-03-17 00:46:12,172] [INFO] Query marker FASTA was written to OceanDNA-b46530/markers.fasta
[2023-03-17 00:46:12,172] [INFO] Task started: Blastn
[2023-03-17 00:46:12,172] [INFO] Running command: blastn -query OceanDNA-b46530/markers.fasta -db /var/lib/cwl/stg10b354e0-26ea-4d78-92f0-f297db91364a/dqc_reference/reference_markers.fasta -out OceanDNA-b46530/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:12,684] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:12,685] [INFO] Selected 10 target genomes.
[2023-03-17 00:46:12,685] [INFO] Target genome list was writen to OceanDNA-b46530/target_genomes.txt
[2023-03-17 00:46:12,691] [INFO] Task started: fastANI
[2023-03-17 00:46:12,691] [INFO] Running command: fastANI --query /var/lib/cwl/stgdac053b3-fd69-4fa8-9c18-d1aac62d7a99/OceanDNA-b46530.fa --refList OceanDNA-b46530/target_genomes.txt --output OceanDNA-b46530/fastani_result.tsv --threads 1
[2023-03-17 00:46:18,832] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:18,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10b354e0-26ea-4d78-92f0-f297db91364a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:18,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10b354e0-26ea-4d78-92f0-f297db91364a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:18,833] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:18,833] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:46:18,833] [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
--------------------------------------------------------------------------------
[2023-03-17 00:46:18,833] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46530/tc_result.tsv
[2023-03-17 00:46:18,833] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:18,833] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:18,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10b354e0-26ea-4d78-92f0-f297db91364a/dqc_reference/checkm_data
[2023-03-17 00:46:18,836] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:18,842] [INFO] Task started: CheckM
[2023-03-17 00:46:18,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46530/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46530/checkm_input OceanDNA-b46530/checkm_result
[2023-03-17 00:47:20,519] [INFO] Task succeeded: CheckM
[2023-03-17 00:47:20,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:47:20,522] [INFO] ===== Completeness check finished =====
[2023-03-17 00:47:20,522] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:47:20,522] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46530/markers.fasta)
[2023-03-17 00:47:20,524] [INFO] Task started: Blastn
[2023-03-17 00:47:20,524] [INFO] Running command: blastn -query OceanDNA-b46530/markers.fasta -db /var/lib/cwl/stg10b354e0-26ea-4d78-92f0-f297db91364a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46530/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:47:21,253] [INFO] Task succeeded: Blastn
[2023-03-17 00:47:21,254] [INFO] Selected 10 target genomes.
[2023-03-17 00:47:21,254] [INFO] Target genome list was writen to OceanDNA-b46530/target_genomes_gtdb.txt
[2023-03-17 00:47:21,612] [INFO] Task started: fastANI
[2023-03-17 00:47:21,613] [INFO] Running command: fastANI --query /var/lib/cwl/stgdac053b3-fd69-4fa8-9c18-d1aac62d7a99/OceanDNA-b46530.fa --refList OceanDNA-b46530/target_genomes_gtdb.txt --output OceanDNA-b46530/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:47:26,656] [INFO] Task succeeded: fastANI
[2023-03-17 00:47:26,662] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:47:26,663] [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_002721375.1	s__UBA1096 sp002721375	98.8852	680	833	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	96.77	96.77	0.62	0.62	2	conclusive
GCA_002686755.1	s__UBA1096 sp002686755	78.159	272	833	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382705.1	s__UBA1096 sp014382705	77.7596	272	833	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002453165.1	s__UBA1096 sp002453165	77.3121	160	833	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	96.70	95.18	0.81	0.76	7	-
GCA_011523195.1	s__UBA1096 sp011523195	77.0348	118	833	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003972865.1	s__UBA1096 sp003972865	76.9843	175	833	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015658765.1	s__UBA1096 sp015658765	76.5643	101	833	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299785.1	s__UBA1096 sp002299785	76.5571	120	833	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689335.1	s__UBA1096 sp002689335	76.5005	86	833	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:47:26,663] [INFO] GTDB search result was written to OceanDNA-b46530/result_gtdb.tsv
[2023-03-17 00:47:26,663] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:47:26,664] [INFO] DFAST_QC result json was written to OceanDNA-b46530/dqc_result.json
[2023-03-17 00:47:26,664] [INFO] DFAST_QC completed!
[2023-03-17 00:47:26,664] [INFO] Total running time: 0h1m39s