[2023-03-18 01:14:00,954] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:14:00,955] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:14:00,955] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe9f52dd-9424-4e40-8287-7be23109454e/dqc_reference
[2023-03-18 01:14:02,093] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:14:02,093] [INFO] Task started: Prodigal
[2023-03-18 01:14:02,093] [INFO] Running command: cat /var/lib/cwl/stgb406c1b6-a418-44ca-a11b-df675dbd7a20/OceanDNA-b14991.fa | prodigal -d OceanDNA-b14991/cds.fna -a OceanDNA-b14991/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:14:08,564] [INFO] Task succeeded: Prodigal
[2023-03-18 01:14:08,565] [INFO] Task started: HMMsearch
[2023-03-18 01:14:08,565] [INFO] Running command: hmmsearch --tblout OceanDNA-b14991/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe9f52dd-9424-4e40-8287-7be23109454e/dqc_reference/reference_markers.hmm OceanDNA-b14991/protein.faa > /dev/null
[2023-03-18 01:14:08,716] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:14:08,716] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb406c1b6-a418-44ca-a11b-df675dbd7a20/OceanDNA-b14991.fa]
[2023-03-18 01:14:08,726] [INFO] Query marker FASTA was written to OceanDNA-b14991/markers.fasta
[2023-03-18 01:14:08,727] [INFO] Task started: Blastn
[2023-03-18 01:14:08,727] [INFO] Running command: blastn -query OceanDNA-b14991/markers.fasta -db /var/lib/cwl/stgfe9f52dd-9424-4e40-8287-7be23109454e/dqc_reference/reference_markers.fasta -out OceanDNA-b14991/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:14:09,222] [INFO] Task succeeded: Blastn
[2023-03-18 01:14:09,222] [INFO] Selected 20 target genomes.
[2023-03-18 01:14:09,223] [INFO] Target genome list was writen to OceanDNA-b14991/target_genomes.txt
[2023-03-18 01:14:09,236] [INFO] Task started: fastANI
[2023-03-18 01:14:09,236] [INFO] Running command: fastANI --query /var/lib/cwl/stgb406c1b6-a418-44ca-a11b-df675dbd7a20/OceanDNA-b14991.fa --refList OceanDNA-b14991/target_genomes.txt --output OceanDNA-b14991/fastani_result.tsv --threads 1
[2023-03-18 01:14:17,619] [INFO] Task succeeded: fastANI
[2023-03-18 01:14:17,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe9f52dd-9424-4e40-8287-7be23109454e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:14:17,620] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe9f52dd-9424-4e40-8287-7be23109454e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:14:17,620] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:14:17,620] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:14:17,620] [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 01:14:17,620] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14991/tc_result.tsv
[2023-03-18 01:14:17,621] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:14:17,621] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:14:17,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe9f52dd-9424-4e40-8287-7be23109454e/dqc_reference/checkm_data
[2023-03-18 01:14:17,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:14:17,626] [INFO] Task started: CheckM
[2023-03-18 01:14:17,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14991/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14991/checkm_input OceanDNA-b14991/checkm_result
[2023-03-18 01:14:39,067] [INFO] Task succeeded: CheckM
[2023-03-18 01:14:39,067] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:14:39,069] [INFO] ===== Completeness check finished =====
[2023-03-18 01:14:39,069] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:14:39,069] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14991/markers.fasta)
[2023-03-18 01:14:39,069] [INFO] Task started: Blastn
[2023-03-18 01:14:39,069] [INFO] Running command: blastn -query OceanDNA-b14991/markers.fasta -db /var/lib/cwl/stgfe9f52dd-9424-4e40-8287-7be23109454e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14991/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:14:39,812] [INFO] Task succeeded: Blastn
[2023-03-18 01:14:39,813] [INFO] Selected 7 target genomes.
[2023-03-18 01:14:39,813] [INFO] Target genome list was writen to OceanDNA-b14991/target_genomes_gtdb.txt
[2023-03-18 01:14:39,825] [INFO] Task started: fastANI
[2023-03-18 01:14:39,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgb406c1b6-a418-44ca-a11b-df675dbd7a20/OceanDNA-b14991.fa --refList OceanDNA-b14991/target_genomes_gtdb.txt --output OceanDNA-b14991/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:14:41,701] [INFO] Task succeeded: fastANI
[2023-03-18 01:14:41,706] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:14:41,706] [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_002703265.1	s__TMED-70 sp002703265	98.3785	383	427	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	97.70	96.59	0.89	0.70	8	conclusive
GCA_002719425.1	s__TMED-70 sp002719425	88.283	318	427	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	-
GCA_002711965.1	s__TMED-70 sp002711965	78.919	214	427	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_002699165.1	s__TMED-70 sp002699165	78.8961	247	427	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_002710135.1	s__TMED-70 sp002710135	78.4198	170	427	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	-
GCA_002171675.1	s__TMED-70 sp002171675	78.1997	161	427	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_009937255.1	s__TMED-70 sp009937255	77.4777	162	427	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	96.35	96.35	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:14:41,706] [INFO] GTDB search result was written to OceanDNA-b14991/result_gtdb.tsv
[2023-03-18 01:14:41,707] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:14:41,707] [INFO] DFAST_QC result json was written to OceanDNA-b14991/dqc_result.json
[2023-03-18 01:14:41,707] [INFO] DFAST_QC completed!
[2023-03-18 01:14:41,707] [INFO] Total running time: 0h0m41s