[2023-03-18 22:54:22,108] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:54:22,108] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:54:22,108] [INFO] DQC Reference Directory: /var/lib/cwl/stge7c31b75-c763-43ba-8120-918492d6ca4d/dqc_reference
[2023-03-18 22:54:23,186] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:54:23,186] [INFO] Task started: Prodigal
[2023-03-18 22:54:23,186] [INFO] Running command: cat /var/lib/cwl/stg45e0dca4-fe50-48e2-89ff-50d772cf1600/OceanDNA-b2136.fa | prodigal -d OceanDNA-b2136/cds.fna -a OceanDNA-b2136/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:54:26,581] [INFO] Task succeeded: Prodigal
[2023-03-18 22:54:26,581] [INFO] Task started: HMMsearch
[2023-03-18 22:54:26,581] [INFO] Running command: hmmsearch --tblout OceanDNA-b2136/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7c31b75-c763-43ba-8120-918492d6ca4d/dqc_reference/reference_markers.hmm OceanDNA-b2136/protein.faa > /dev/null
[2023-03-18 22:54:26,704] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:54:26,705] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg45e0dca4-fe50-48e2-89ff-50d772cf1600/OceanDNA-b2136.fa]
[2023-03-18 22:54:26,711] [INFO] Query marker FASTA was written to OceanDNA-b2136/markers.fasta
[2023-03-18 22:54:26,712] [INFO] Task started: Blastn
[2023-03-18 22:54:26,712] [INFO] Running command: blastn -query OceanDNA-b2136/markers.fasta -db /var/lib/cwl/stge7c31b75-c763-43ba-8120-918492d6ca4d/dqc_reference/reference_markers.fasta -out OceanDNA-b2136/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:54:27,270] [INFO] Task succeeded: Blastn
[2023-03-18 22:54:27,271] [INFO] Selected 7 target genomes.
[2023-03-18 22:54:27,271] [INFO] Target genome list was writen to OceanDNA-b2136/target_genomes.txt
[2023-03-18 22:54:27,274] [INFO] Task started: fastANI
[2023-03-18 22:54:27,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg45e0dca4-fe50-48e2-89ff-50d772cf1600/OceanDNA-b2136.fa --refList OceanDNA-b2136/target_genomes.txt --output OceanDNA-b2136/fastani_result.tsv --threads 1
[2023-03-18 22:54:29,695] [INFO] Task succeeded: fastANI
[2023-03-18 22:54:29,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7c31b75-c763-43ba-8120-918492d6ca4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:54:29,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7c31b75-c763-43ba-8120-918492d6ca4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:54:29,696] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:54:29,696] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:54:29,696] [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 22:54:29,696] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2136/tc_result.tsv
[2023-03-18 22:54:29,696] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:54:29,696] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:54:29,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7c31b75-c763-43ba-8120-918492d6ca4d/dqc_reference/checkm_data
[2023-03-18 22:54:29,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:54:29,701] [INFO] Task started: CheckM
[2023-03-18 22:54:29,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2136/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2136/checkm_input OceanDNA-b2136/checkm_result
[2023-03-18 22:54:44,656] [INFO] Task succeeded: CheckM
[2023-03-18 22:54:44,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:54:44,661] [INFO] ===== Completeness check finished =====
[2023-03-18 22:54:44,661] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:54:44,661] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2136/markers.fasta)
[2023-03-18 22:54:44,663] [INFO] Task started: Blastn
[2023-03-18 22:54:44,664] [INFO] Running command: blastn -query OceanDNA-b2136/markers.fasta -db /var/lib/cwl/stge7c31b75-c763-43ba-8120-918492d6ca4d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2136/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:54:45,278] [INFO] Task succeeded: Blastn
[2023-03-18 22:54:45,279] [INFO] Selected 5 target genomes.
[2023-03-18 22:54:45,279] [INFO] Target genome list was writen to OceanDNA-b2136/target_genomes_gtdb.txt
[2023-03-18 22:54:45,285] [INFO] Task started: fastANI
[2023-03-18 22:54:45,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg45e0dca4-fe50-48e2-89ff-50d772cf1600/OceanDNA-b2136.fa --refList OceanDNA-b2136/target_genomes_gtdb.txt --output OceanDNA-b2136/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:54:46,234] [INFO] Task succeeded: fastANI
[2023-03-18 22:54:46,238] [INFO] Found 5 fastANI hits (4 hits with ANI > circumscription radius)
[2023-03-18 22:54:46,238] [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_902604835.1	s__Actinomarina sp902604835	95.9819	169	217	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.34	95.34	0.81	0.81	2	inconclusive
GCA_902533795.1	s__Actinomarina sp902533795	95.8379	185	217	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.75	95.75	0.81	0.81	2	inconclusive
GCA_902519845.1	s__Actinomarina sp902519845	95.4324	198	217	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.50	95.50	0.91	0.91	2	inconclusive
GCA_902571385.1	s__Actinomarina sp902571385	95.1677	183	217	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.95	95.63	0.85	0.83	4	inconclusive
GCA_902609285.1	s__Actinomarina sp902609285	93.8948	161	217	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:54:46,238] [INFO] GTDB search result was written to OceanDNA-b2136/result_gtdb.tsv
[2023-03-18 22:54:46,238] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:54:46,239] [INFO] DFAST_QC result json was written to OceanDNA-b2136/dqc_result.json
[2023-03-18 22:54:46,239] [INFO] DFAST_QC completed!
[2023-03-18 22:54:46,239] [INFO] Total running time: 0h0m24s