[2023-03-18 22:24:43,955] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:24:43,955] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:24:43,955] [INFO] DQC Reference Directory: /var/lib/cwl/stge8e4613f-6e31-4c6a-941a-5f3ea48b839b/dqc_reference
[2023-03-18 22:24:45,033] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:24:45,033] [INFO] Task started: Prodigal
[2023-03-18 22:24:45,033] [INFO] Running command: cat /var/lib/cwl/stgd9589890-be42-4e10-8007-c9eb7f691f2b/OceanDNA-b23216.fa | prodigal -d OceanDNA-b23216/cds.fna -a OceanDNA-b23216/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:25:05,277] [INFO] Task succeeded: Prodigal
[2023-03-18 22:25:05,277] [INFO] Task started: HMMsearch
[2023-03-18 22:25:05,277] [INFO] Running command: hmmsearch --tblout OceanDNA-b23216/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8e4613f-6e31-4c6a-941a-5f3ea48b839b/dqc_reference/reference_markers.hmm OceanDNA-b23216/protein.faa > /dev/null
[2023-03-18 22:25:05,479] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:25:05,480] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd9589890-be42-4e10-8007-c9eb7f691f2b/OceanDNA-b23216.fa]
[2023-03-18 22:25:05,505] [INFO] Query marker FASTA was written to OceanDNA-b23216/markers.fasta
[2023-03-18 22:25:05,505] [INFO] Task started: Blastn
[2023-03-18 22:25:05,505] [INFO] Running command: blastn -query OceanDNA-b23216/markers.fasta -db /var/lib/cwl/stge8e4613f-6e31-4c6a-941a-5f3ea48b839b/dqc_reference/reference_markers.fasta -out OceanDNA-b23216/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:25:05,939] [INFO] Task succeeded: Blastn
[2023-03-18 22:25:05,940] [INFO] Selected 10 target genomes.
[2023-03-18 22:25:05,940] [INFO] Target genome list was writen to OceanDNA-b23216/target_genomes.txt
[2023-03-18 22:25:05,947] [INFO] Task started: fastANI
[2023-03-18 22:25:05,947] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9589890-be42-4e10-8007-c9eb7f691f2b/OceanDNA-b23216.fa --refList OceanDNA-b23216/target_genomes.txt --output OceanDNA-b23216/fastani_result.tsv --threads 1
[2023-03-18 22:25:09,882] [INFO] Task succeeded: fastANI
[2023-03-18 22:25:09,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8e4613f-6e31-4c6a-941a-5f3ea48b839b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:25:09,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8e4613f-6e31-4c6a-941a-5f3ea48b839b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:25:09,883] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:25:09,883] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:25:09,883] [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 22:25:09,883] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23216/tc_result.tsv
[2023-03-18 22:25:09,884] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:25:09,884] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:25:09,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8e4613f-6e31-4c6a-941a-5f3ea48b839b/dqc_reference/checkm_data
[2023-03-18 22:25:09,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:25:09,892] [INFO] Task started: CheckM
[2023-03-18 22:25:09,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23216/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23216/checkm_input OceanDNA-b23216/checkm_result
[2023-03-18 22:26:02,084] [INFO] Task succeeded: CheckM
[2023-03-18 22:26:02,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 22:26:02,087] [INFO] ===== Completeness check finished =====
[2023-03-18 22:26:02,088] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:26:02,088] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23216/markers.fasta)
[2023-03-18 22:26:02,088] [INFO] Task started: Blastn
[2023-03-18 22:26:02,088] [INFO] Running command: blastn -query OceanDNA-b23216/markers.fasta -db /var/lib/cwl/stge8e4613f-6e31-4c6a-941a-5f3ea48b839b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23216/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:26:02,480] [INFO] Task succeeded: Blastn
[2023-03-18 22:26:02,481] [INFO] Selected 11 target genomes.
[2023-03-18 22:26:02,481] [INFO] Target genome list was writen to OceanDNA-b23216/target_genomes_gtdb.txt
[2023-03-18 22:26:02,494] [INFO] Task started: fastANI
[2023-03-18 22:26:02,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9589890-be42-4e10-8007-c9eb7f691f2b/OceanDNA-b23216.fa --refList OceanDNA-b23216/target_genomes_gtdb.txt --output OceanDNA-b23216/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:26:08,856] [INFO] Task succeeded: fastANI
[2023-03-18 22:26:08,859] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:26:08,859] [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_002729015.1	s__TMED15 sp002729015	98.7805	1201	1278	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__UBA9662;g__TMED15	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002714785.1	s__TMED15 sp002714785	91.6304	1123	1278	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__UBA9662;g__TMED15	95.0	97.64	97.01	0.88	0.83	5	-
--------------------------------------------------------------------------------
[2023-03-18 22:26:08,859] [INFO] GTDB search result was written to OceanDNA-b23216/result_gtdb.tsv
[2023-03-18 22:26:08,859] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:26:08,860] [INFO] DFAST_QC result json was written to OceanDNA-b23216/dqc_result.json
[2023-03-18 22:26:08,860] [INFO] DFAST_QC completed!
[2023-03-18 22:26:08,860] [INFO] Total running time: 0h1m25s