[2023-03-17 22:57:28,030] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:57:28,030] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:57:28,031] [INFO] DQC Reference Directory: /var/lib/cwl/stgd48ff080-9fbd-45c7-ae00-90be484b7785/dqc_reference
[2023-03-17 22:57:29,174] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:57:29,174] [INFO] Task started: Prodigal
[2023-03-17 22:57:29,174] [INFO] Running command: cat /var/lib/cwl/stg30e0e8dc-eecb-42d0-bf55-d81aad46f700/OceanDNA-b21010.fa | prodigal -d OceanDNA-b21010/cds.fna -a OceanDNA-b21010/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:57:48,110] [INFO] Task succeeded: Prodigal
[2023-03-17 22:57:48,110] [INFO] Task started: HMMsearch
[2023-03-17 22:57:48,110] [INFO] Running command: hmmsearch --tblout OceanDNA-b21010/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd48ff080-9fbd-45c7-ae00-90be484b7785/dqc_reference/reference_markers.hmm OceanDNA-b21010/protein.faa > /dev/null
[2023-03-17 22:57:48,306] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:57:48,307] [INFO] Found 6/6 markers.
[2023-03-17 22:57:48,333] [INFO] Query marker FASTA was written to OceanDNA-b21010/markers.fasta
[2023-03-17 22:57:48,334] [INFO] Task started: Blastn
[2023-03-17 22:57:48,334] [INFO] Running command: blastn -query OceanDNA-b21010/markers.fasta -db /var/lib/cwl/stgd48ff080-9fbd-45c7-ae00-90be484b7785/dqc_reference/reference_markers.fasta -out OceanDNA-b21010/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:57:48,865] [INFO] Task succeeded: Blastn
[2023-03-17 22:57:48,866] [INFO] Selected 22 target genomes.
[2023-03-17 22:57:48,866] [INFO] Target genome list was writen to OceanDNA-b21010/target_genomes.txt
[2023-03-17 22:57:48,882] [INFO] Task started: fastANI
[2023-03-17 22:57:48,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg30e0e8dc-eecb-42d0-bf55-d81aad46f700/OceanDNA-b21010.fa --refList OceanDNA-b21010/target_genomes.txt --output OceanDNA-b21010/fastani_result.tsv --threads 1
[2023-03-17 22:58:01,613] [INFO] Task succeeded: fastANI
[2023-03-17 22:58:01,613] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd48ff080-9fbd-45c7-ae00-90be484b7785/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:58:01,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd48ff080-9fbd-45c7-ae00-90be484b7785/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:58:01,613] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:58:01,613] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 22:58:01,613] [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 22:58:01,615] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21010/tc_result.tsv
[2023-03-17 22:58:01,615] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:58:01,615] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:58:01,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd48ff080-9fbd-45c7-ae00-90be484b7785/dqc_reference/checkm_data
[2023-03-17 22:58:01,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:58:01,643] [INFO] Task started: CheckM
[2023-03-17 22:58:01,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21010/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21010/checkm_input OceanDNA-b21010/checkm_result
[2023-03-17 22:58:49,334] [INFO] Task succeeded: CheckM
[2023-03-17 22:58:49,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 22:58:49,336] [INFO] ===== Completeness check finished =====
[2023-03-17 22:58:49,337] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:58:49,337] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21010/markers.fasta)
[2023-03-17 22:58:49,338] [INFO] Task started: Blastn
[2023-03-17 22:58:49,338] [INFO] Running command: blastn -query OceanDNA-b21010/markers.fasta -db /var/lib/cwl/stgd48ff080-9fbd-45c7-ae00-90be484b7785/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21010/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:58:50,105] [INFO] Task succeeded: Blastn
[2023-03-17 22:58:50,105] [INFO] Selected 29 target genomes.
[2023-03-17 22:58:50,106] [INFO] Target genome list was writen to OceanDNA-b21010/target_genomes_gtdb.txt
[2023-03-17 22:58:50,131] [INFO] Task started: fastANI
[2023-03-17 22:58:50,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg30e0e8dc-eecb-42d0-bf55-d81aad46f700/OceanDNA-b21010.fa --refList OceanDNA-b21010/target_genomes_gtdb.txt --output OceanDNA-b21010/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:59:07,895] [INFO] Task succeeded: fastANI
[2023-03-17 22:59:07,899] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:59:07,899] [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_013215615.1	s__JABSQX01 sp013215615	76.2788	107	1033	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	75.9031	92	1033	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	75.9016	97	1033	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729515.1	s__GCA-2729515 sp002729515	75.8791	75	1033	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__GCA-2729515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719955.1	s__UBA4427 sp002719955	75.2943	52	1033	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:59:07,899] [INFO] GTDB search result was written to OceanDNA-b21010/result_gtdb.tsv
[2023-03-17 22:59:07,899] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:59:07,900] [INFO] DFAST_QC result json was written to OceanDNA-b21010/dqc_result.json
[2023-03-17 22:59:07,900] [INFO] DFAST_QC completed!
[2023-03-17 22:59:07,901] [INFO] Total running time: 0h1m40s