[2023-03-17 23:20:45,998] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:20:45,998] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:20:45,998] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3fa5930-a977-4c1b-83d9-f1b2ba08f97c/dqc_reference
[2023-03-17 23:20:47,117] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:20:47,117] [INFO] Task started: Prodigal
[2023-03-17 23:20:47,117] [INFO] Running command: cat /var/lib/cwl/stg9f431c06-ca7c-4e84-a951-16ca5acf9508/OceanDNA-b19607.fa | prodigal -d OceanDNA-b19607/cds.fna -a OceanDNA-b19607/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:20:53,593] [INFO] Task succeeded: Prodigal
[2023-03-17 23:20:53,594] [INFO] Task started: HMMsearch
[2023-03-17 23:20:53,594] [INFO] Running command: hmmsearch --tblout OceanDNA-b19607/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3fa5930-a977-4c1b-83d9-f1b2ba08f97c/dqc_reference/reference_markers.hmm OceanDNA-b19607/protein.faa > /dev/null
[2023-03-17 23:20:53,720] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:20:53,720] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9f431c06-ca7c-4e84-a951-16ca5acf9508/OceanDNA-b19607.fa]
[2023-03-17 23:20:53,737] [INFO] Query marker FASTA was written to OceanDNA-b19607/markers.fasta
[2023-03-17 23:20:53,739] [INFO] Task started: Blastn
[2023-03-17 23:20:53,739] [INFO] Running command: blastn -query OceanDNA-b19607/markers.fasta -db /var/lib/cwl/stgb3fa5930-a977-4c1b-83d9-f1b2ba08f97c/dqc_reference/reference_markers.fasta -out OceanDNA-b19607/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:20:54,261] [INFO] Task succeeded: Blastn
[2023-03-17 23:20:54,263] [INFO] Selected 11 target genomes.
[2023-03-17 23:20:54,264] [INFO] Target genome list was writen to OceanDNA-b19607/target_genomes.txt
[2023-03-17 23:20:54,271] [INFO] Task started: fastANI
[2023-03-17 23:20:54,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f431c06-ca7c-4e84-a951-16ca5acf9508/OceanDNA-b19607.fa --refList OceanDNA-b19607/target_genomes.txt --output OceanDNA-b19607/fastani_result.tsv --threads 1
[2023-03-17 23:20:58,236] [INFO] Task succeeded: fastANI
[2023-03-17 23:20:58,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3fa5930-a977-4c1b-83d9-f1b2ba08f97c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:20:58,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3fa5930-a977-4c1b-83d9-f1b2ba08f97c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:20:58,237] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:20:58,237] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:20:58,237] [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 23:20:58,237] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19607/tc_result.tsv
[2023-03-17 23:20:58,237] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:20:58,237] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:20:58,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3fa5930-a977-4c1b-83d9-f1b2ba08f97c/dqc_reference/checkm_data
[2023-03-17 23:20:58,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:20:58,251] [INFO] Task started: CheckM
[2023-03-17 23:20:58,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19607/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19607/checkm_input OceanDNA-b19607/checkm_result
[2023-03-17 23:21:19,925] [INFO] Task succeeded: CheckM
[2023-03-17 23:21:19,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:21:19,929] [INFO] ===== Completeness check finished =====
[2023-03-17 23:21:19,929] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:21:19,929] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19607/markers.fasta)
[2023-03-17 23:21:19,931] [INFO] Task started: Blastn
[2023-03-17 23:21:19,931] [INFO] Running command: blastn -query OceanDNA-b19607/markers.fasta -db /var/lib/cwl/stgb3fa5930-a977-4c1b-83d9-f1b2ba08f97c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19607/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:21:20,498] [INFO] Task succeeded: Blastn
[2023-03-17 23:21:20,499] [INFO] Selected 15 target genomes.
[2023-03-17 23:21:20,499] [INFO] Target genome list was writen to OceanDNA-b19607/target_genomes_gtdb.txt
[2023-03-17 23:21:20,712] [INFO] Task started: fastANI
[2023-03-17 23:21:20,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f431c06-ca7c-4e84-a951-16ca5acf9508/OceanDNA-b19607.fa --refList OceanDNA-b19607/target_genomes_gtdb.txt --output OceanDNA-b19607/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:21:24,841] [INFO] Task succeeded: fastANI
[2023-03-17 23:21:24,845] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:21:24,845] [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_002169695.1	s__TMED80 sp002169695	76.9518	58	437	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713885.1	s__TMED80 sp002713885	76.6335	69	437	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645565.1	s__TMED80 sp018645565	76.5625	77	437	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	99.41	99.35	0.85	0.81	6	-
GCA_004321745.1	s__TMED80 sp002170405	76.5303	71	437	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	99.32	99.32	0.73	0.73	2	-
GCA_905478065.1	s__TMED80 sp905478065	76.2456	89	437	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:21:24,846] [INFO] GTDB search result was written to OceanDNA-b19607/result_gtdb.tsv
[2023-03-17 23:21:24,846] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:21:24,846] [INFO] DFAST_QC result json was written to OceanDNA-b19607/dqc_result.json
[2023-03-17 23:21:24,846] [INFO] DFAST_QC completed!
[2023-03-17 23:21:24,846] [INFO] Total running time: 0h0m39s