[2023-03-14 13:48:47,256] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:48:47,257] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:48:47,257] [INFO] DQC Reference Directory: /var/lib/cwl/stge4133490-4a0a-42a4-9a09-eedc8821fa2b/dqc_reference
[2023-03-14 13:48:48,542] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:48:48,543] [INFO] Task started: Prodigal
[2023-03-14 13:48:48,543] [INFO] Running command: cat /var/lib/cwl/stg2fc2b46f-106d-41df-83fb-479bd462014a/OceanDNA-b22653.fa | prodigal -d OceanDNA-b22653/cds.fna -a OceanDNA-b22653/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:49:04,477] [INFO] Task succeeded: Prodigal
[2023-03-14 13:49:04,478] [INFO] Task started: HMMsearch
[2023-03-14 13:49:04,478] [INFO] Running command: hmmsearch --tblout OceanDNA-b22653/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4133490-4a0a-42a4-9a09-eedc8821fa2b/dqc_reference/reference_markers.hmm OceanDNA-b22653/protein.faa > /dev/null
[2023-03-14 13:49:04,867] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:49:04,868] [INFO] Found 6/6 markers.
[2023-03-14 13:49:04,888] [INFO] Query marker FASTA was written to OceanDNA-b22653/markers.fasta
[2023-03-14 13:49:04,895] [INFO] Task started: Blastn
[2023-03-14 13:49:04,895] [INFO] Running command: blastn -query OceanDNA-b22653/markers.fasta -db /var/lib/cwl/stge4133490-4a0a-42a4-9a09-eedc8821fa2b/dqc_reference/reference_markers.fasta -out OceanDNA-b22653/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:49:05,910] [INFO] Task succeeded: Blastn
[2023-03-14 13:49:05,910] [INFO] Selected 19 target genomes.
[2023-03-14 13:49:05,911] [INFO] Target genome list was writen to OceanDNA-b22653/target_genomes.txt
[2023-03-14 13:49:05,929] [INFO] Task started: fastANI
[2023-03-14 13:49:05,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fc2b46f-106d-41df-83fb-479bd462014a/OceanDNA-b22653.fa --refList OceanDNA-b22653/target_genomes.txt --output OceanDNA-b22653/fastani_result.tsv --threads 1
[2023-03-14 13:49:25,584] [INFO] Task succeeded: fastANI
[2023-03-14 13:49:25,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4133490-4a0a-42a4-9a09-eedc8821fa2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:49:25,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4133490-4a0a-42a4-9a09-eedc8821fa2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:49:25,585] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:49:25,585] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:49:25,585] [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
--------------------------------------------------------------------------------
[2023-03-14 13:49:25,585] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22653/tc_result.tsv
[2023-03-14 13:49:25,586] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:49:25,586] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:49:25,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4133490-4a0a-42a4-9a09-eedc8821fa2b/dqc_reference/checkm_data
[2023-03-14 13:49:25,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:49:25,700] [INFO] Task started: CheckM
[2023-03-14 13:49:25,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22653/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22653/checkm_input OceanDNA-b22653/checkm_result
[2023-03-14 13:50:02,612] [INFO] Task succeeded: CheckM
[2023-03-14 13:50:02,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.01%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:50:02,616] [INFO] ===== Completeness check finished =====
[2023-03-14 13:50:02,616] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:50:02,616] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22653/markers.fasta)
[2023-03-14 13:50:02,617] [INFO] Task started: Blastn
[2023-03-14 13:50:02,617] [INFO] Running command: blastn -query OceanDNA-b22653/markers.fasta -db /var/lib/cwl/stge4133490-4a0a-42a4-9a09-eedc8821fa2b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22653/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:50:04,572] [INFO] Task succeeded: Blastn
[2023-03-14 13:50:04,573] [INFO] Selected 19 target genomes.
[2023-03-14 13:50:04,573] [INFO] Target genome list was writen to OceanDNA-b22653/target_genomes_gtdb.txt
[2023-03-14 13:50:04,599] [INFO] Task started: fastANI
[2023-03-14 13:50:04,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fc2b46f-106d-41df-83fb-479bd462014a/OceanDNA-b22653.fa --refList OceanDNA-b22653/target_genomes_gtdb.txt --output OceanDNA-b22653/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:50:17,730] [INFO] Task succeeded: fastANI
[2023-03-14 13:50:17,739] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:50:17,740] [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_018970605.1	s__QWPN01 sp018970605	78.5913	148	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926295.1	s__RGVT01 sp009926295	78.5126	179	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919035.1	s__QWPN01 sp903919035	78.5073	156	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_010027105.1	s__RGVT01 sp010027105	78.4145	154	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872925.1	s__QWPN01 sp016872925	78.3557	168	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923125.1	s__RGVT01 sp009923125	78.2866	137	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670825.1	s__QWPN01 sp003670825	78.2794	108	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853835.1	s__QWPN01 sp017853835	78.1821	135	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831155.1	s__QWPN01 sp903831155	78.0362	179	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789975.1	s__QWPN01 sp005789975	78.0173	124	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.49	99.44	0.83	0.81	3	-
GCA_014192425.1	s__QWPN01 sp014192425	77.9591	176	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671185.1	s__QWPN01 sp003671185	77.9434	143	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002405515.1	s__UBA4655 sp002405515	77.899	149	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA4655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958265.1	s__QWPN01 sp903958265	77.8864	136	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.26	98.26	0.80	0.80	2	-
GCA_903951635.1	s__QWOP01 sp903951635	77.5613	144	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	99.54	99.51	0.90	0.90	3	-
GCA_009691925.1	s__QWOP01 sp009691925	77.4427	98	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924545.1	s__F1-20-MAGs016 sp009924545	77.3268	135	438	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:50:17,784] [INFO] GTDB search result was written to OceanDNA-b22653/result_gtdb.tsv
[2023-03-14 13:50:17,785] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:50:17,786] [INFO] DFAST_QC result json was written to OceanDNA-b22653/dqc_result.json
[2023-03-14 13:50:17,786] [INFO] DFAST_QC completed!
[2023-03-14 13:50:17,786] [INFO] Total running time: 0h1m31s