[2023-03-16 04:24:46,335] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:24:46,336] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:24:46,336] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5d6e891-a2c3-40e9-975f-22910edf93fb/dqc_reference
[2023-03-16 04:24:48,115] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:24:48,115] [INFO] Task started: Prodigal
[2023-03-16 04:24:48,115] [INFO] Running command: cat /var/lib/cwl/stg45127ae5-5017-41dc-b45b-2a0622c65f6a/OceanDNA-b16838.fa | prodigal -d OceanDNA-b16838/cds.fna -a OceanDNA-b16838/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:24:51,691] [INFO] Task succeeded: Prodigal
[2023-03-16 04:24:51,691] [INFO] Task started: HMMsearch
[2023-03-16 04:24:51,691] [INFO] Running command: hmmsearch --tblout OceanDNA-b16838/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5d6e891-a2c3-40e9-975f-22910edf93fb/dqc_reference/reference_markers.hmm OceanDNA-b16838/protein.faa > /dev/null
[2023-03-16 04:24:51,878] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:24:51,878] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg45127ae5-5017-41dc-b45b-2a0622c65f6a/OceanDNA-b16838.fa]
[2023-03-16 04:24:51,885] [INFO] Query marker FASTA was written to OceanDNA-b16838/markers.fasta
[2023-03-16 04:24:51,885] [INFO] Task started: Blastn
[2023-03-16 04:24:51,885] [INFO] Running command: blastn -query OceanDNA-b16838/markers.fasta -db /var/lib/cwl/stgd5d6e891-a2c3-40e9-975f-22910edf93fb/dqc_reference/reference_markers.fasta -out OceanDNA-b16838/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:24:53,366] [INFO] Task succeeded: Blastn
[2023-03-16 04:24:53,367] [INFO] Selected 15 target genomes.
[2023-03-16 04:24:53,367] [INFO] Target genome list was writen to OceanDNA-b16838/target_genomes.txt
[2023-03-16 04:24:53,376] [INFO] Task started: fastANI
[2023-03-16 04:24:53,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg45127ae5-5017-41dc-b45b-2a0622c65f6a/OceanDNA-b16838.fa --refList OceanDNA-b16838/target_genomes.txt --output OceanDNA-b16838/fastani_result.tsv --threads 1
[2023-03-16 04:25:00,013] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:00,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5d6e891-a2c3-40e9-975f-22910edf93fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:25:00,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5d6e891-a2c3-40e9-975f-22910edf93fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:25:00,014] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:25:00,014] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:25:00,014] [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
--------------------------------------------------------------------------------
[2023-03-16 04:25:00,014] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16838/tc_result.tsv
[2023-03-16 04:25:00,015] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:25:00,015] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:25:00,015] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5d6e891-a2c3-40e9-975f-22910edf93fb/dqc_reference/checkm_data
[2023-03-16 04:25:00,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:25:00,020] [INFO] Task started: CheckM
[2023-03-16 04:25:00,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16838/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16838/checkm_input OceanDNA-b16838/checkm_result
[2023-03-16 04:25:15,900] [INFO] Task succeeded: CheckM
[2023-03-16 04:25:15,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:25:15,902] [INFO] ===== Completeness check finished =====
[2023-03-16 04:25:15,902] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:25:15,902] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16838/markers.fasta)
[2023-03-16 04:25:15,903] [INFO] Task started: Blastn
[2023-03-16 04:25:15,904] [INFO] Running command: blastn -query OceanDNA-b16838/markers.fasta -db /var/lib/cwl/stgd5d6e891-a2c3-40e9-975f-22910edf93fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16838/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:16,348] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:16,349] [INFO] Selected 10 target genomes.
[2023-03-16 04:25:16,349] [INFO] Target genome list was writen to OceanDNA-b16838/target_genomes_gtdb.txt
[2023-03-16 04:25:16,363] [INFO] Task started: fastANI
[2023-03-16 04:25:16,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg45127ae5-5017-41dc-b45b-2a0622c65f6a/OceanDNA-b16838.fa --refList OceanDNA-b16838/target_genomes_gtdb.txt --output OceanDNA-b16838/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:25:18,528] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:18,531] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:25:18,532] [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_902609885.1	s__GCA-002715585 sp902609885	95.3244	224	232	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__GCA-002715585	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002715585.2	s__GCA-002715585 sp002715585	92.7825	220	232	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__GCA-002715585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697665.2	s__GCA-002715585 sp002697665	88.2982	200	232	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__GCA-002715585	95.0	96.81	96.81	0.86	0.86	2	-
GCA_002701605.2	s__TMED126 sp002701605	77.959	72	232	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED126	95.0	95.74	95.73	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-16 04:25:18,532] [INFO] GTDB search result was written to OceanDNA-b16838/result_gtdb.tsv
[2023-03-16 04:25:18,532] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:25:18,532] [INFO] DFAST_QC result json was written to OceanDNA-b16838/dqc_result.json
[2023-03-16 04:25:18,533] [INFO] DFAST_QC completed!
[2023-03-16 04:25:18,533] [INFO] Total running time: 0h0m32s