[2023-03-18 02:42:32,869] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:42:32,869] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:42:32,869] [INFO] DQC Reference Directory: /var/lib/cwl/stg6115c306-ead2-4c66-80ea-8f50a419b6ac/dqc_reference
[2023-03-18 02:42:34,115] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:42:34,116] [INFO] Task started: Prodigal
[2023-03-18 02:42:34,117] [INFO] Running command: cat /var/lib/cwl/stg3feed19f-da75-4094-b38c-e54c579bf624/OceanDNA-b15074.fa | prodigal -d OceanDNA-b15074/cds.fna -a OceanDNA-b15074/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:42:39,488] [INFO] Task succeeded: Prodigal
[2023-03-18 02:42:39,488] [INFO] Task started: HMMsearch
[2023-03-18 02:42:39,488] [INFO] Running command: hmmsearch --tblout OceanDNA-b15074/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6115c306-ead2-4c66-80ea-8f50a419b6ac/dqc_reference/reference_markers.hmm OceanDNA-b15074/protein.faa > /dev/null
[2023-03-18 02:42:39,651] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:42:39,651] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3feed19f-da75-4094-b38c-e54c579bf624/OceanDNA-b15074.fa]
[2023-03-18 02:42:39,660] [INFO] Query marker FASTA was written to OceanDNA-b15074/markers.fasta
[2023-03-18 02:42:39,660] [INFO] Task started: Blastn
[2023-03-18 02:42:39,660] [INFO] Running command: blastn -query OceanDNA-b15074/markers.fasta -db /var/lib/cwl/stg6115c306-ead2-4c66-80ea-8f50a419b6ac/dqc_reference/reference_markers.fasta -out OceanDNA-b15074/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:42:40,140] [INFO] Task succeeded: Blastn
[2023-03-18 02:42:40,141] [INFO] Selected 10 target genomes.
[2023-03-18 02:42:40,141] [INFO] Target genome list was writen to OceanDNA-b15074/target_genomes.txt
[2023-03-18 02:42:40,145] [INFO] Task started: fastANI
[2023-03-18 02:42:40,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg3feed19f-da75-4094-b38c-e54c579bf624/OceanDNA-b15074.fa --refList OceanDNA-b15074/target_genomes.txt --output OceanDNA-b15074/fastani_result.tsv --threads 1
[2023-03-18 02:42:43,812] [INFO] Task succeeded: fastANI
[2023-03-18 02:42:43,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6115c306-ead2-4c66-80ea-8f50a419b6ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:42:43,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6115c306-ead2-4c66-80ea-8f50a419b6ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:42:43,813] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:42:43,813] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:42:43,813] [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 02:42:43,813] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15074/tc_result.tsv
[2023-03-18 02:42:43,813] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:42:43,813] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:42:43,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6115c306-ead2-4c66-80ea-8f50a419b6ac/dqc_reference/checkm_data
[2023-03-18 02:42:43,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:42:43,818] [INFO] Task started: CheckM
[2023-03-18 02:42:43,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15074/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15074/checkm_input OceanDNA-b15074/checkm_result
[2023-03-18 02:43:02,726] [INFO] Task succeeded: CheckM
[2023-03-18 02:43:02,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:43:02,728] [INFO] ===== Completeness check finished =====
[2023-03-18 02:43:02,728] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:43:02,728] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15074/markers.fasta)
[2023-03-18 02:43:02,728] [INFO] Task started: Blastn
[2023-03-18 02:43:02,728] [INFO] Running command: blastn -query OceanDNA-b15074/markers.fasta -db /var/lib/cwl/stg6115c306-ead2-4c66-80ea-8f50a419b6ac/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15074/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:43:03,358] [INFO] Task succeeded: Blastn
[2023-03-18 02:43:03,358] [INFO] Selected 13 target genomes.
[2023-03-18 02:43:03,359] [INFO] Target genome list was writen to OceanDNA-b15074/target_genomes_gtdb.txt
[2023-03-18 02:43:03,576] [INFO] Task started: fastANI
[2023-03-18 02:43:03,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg3feed19f-da75-4094-b38c-e54c579bf624/OceanDNA-b15074.fa --refList OceanDNA-b15074/target_genomes_gtdb.txt --output OceanDNA-b15074/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:43:06,669] [INFO] Task succeeded: fastANI
[2023-03-18 02:43:06,673] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:43:06,673] [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_002721875.1	s__TMED-70 sp002721875	97.4836	287	361	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	conclusive
GCA_008373205.1	s__TMED-70 sp008373205	81.2729	258	361	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_002171675.1	s__TMED-70 sp002171675	81.1981	247	361	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_002699165.1	s__TMED-70 sp002699165	77.5255	147	361	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_002711965.1	s__TMED-70 sp002711965	77.0381	115	361	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	98.97	98.97	0.82	0.82	2	-
GCA_002710135.1	s__TMED-70 sp002710135	76.9967	96	361	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	-
--------------------------------------------------------------------------------
[2023-03-18 02:43:06,673] [INFO] GTDB search result was written to OceanDNA-b15074/result_gtdb.tsv
[2023-03-18 02:43:06,674] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:43:06,674] [INFO] DFAST_QC result json was written to OceanDNA-b15074/dqc_result.json
[2023-03-18 02:43:06,674] [INFO] DFAST_QC completed!
[2023-03-18 02:43:06,674] [INFO] Total running time: 0h0m34s