[2023-03-15 14:06:11,186] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:06:11,186] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:06:11,186] [INFO] DQC Reference Directory: /var/lib/cwl/stg524f74a5-3fa9-4538-adf8-1342a5df2df7/dqc_reference
[2023-03-15 14:06:12,289] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:06:12,290] [INFO] Task started: Prodigal
[2023-03-15 14:06:12,290] [INFO] Running command: cat /var/lib/cwl/stg8f20154f-a688-4efa-8036-7b935acdaaac/OceanDNA-b3635.fa | prodigal -d OceanDNA-b3635/cds.fna -a OceanDNA-b3635/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:07:21,496] [INFO] Task succeeded: Prodigal
[2023-03-15 14:07:21,496] [INFO] Task started: HMMsearch
[2023-03-15 14:07:21,496] [INFO] Running command: hmmsearch --tblout OceanDNA-b3635/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg524f74a5-3fa9-4538-adf8-1342a5df2df7/dqc_reference/reference_markers.hmm OceanDNA-b3635/protein.faa > /dev/null
[2023-03-15 14:07:21,811] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:07:21,812] [INFO] Found 6/6 markers.
[2023-03-15 14:07:21,859] [INFO] Query marker FASTA was written to OceanDNA-b3635/markers.fasta
[2023-03-15 14:07:21,861] [INFO] Task started: Blastn
[2023-03-15 14:07:21,861] [INFO] Running command: blastn -query OceanDNA-b3635/markers.fasta -db /var/lib/cwl/stg524f74a5-3fa9-4538-adf8-1342a5df2df7/dqc_reference/reference_markers.fasta -out OceanDNA-b3635/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:07:22,388] [INFO] Task succeeded: Blastn
[2023-03-15 14:07:22,389] [INFO] Selected 34 target genomes.
[2023-03-15 14:07:22,389] [INFO] Target genome list was writen to OceanDNA-b3635/target_genomes.txt
[2023-03-15 14:07:22,410] [INFO] Task started: fastANI
[2023-03-15 14:07:22,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f20154f-a688-4efa-8036-7b935acdaaac/OceanDNA-b3635.fa --refList OceanDNA-b3635/target_genomes.txt --output OceanDNA-b3635/fastani_result.tsv --threads 1
[2023-03-15 14:07:50,993] [INFO] Task succeeded: fastANI
[2023-03-15 14:07:50,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg524f74a5-3fa9-4538-adf8-1342a5df2df7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:07:50,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg524f74a5-3fa9-4538-adf8-1342a5df2df7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:07:50,994] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:07:50,994] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:07:50,994] [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
--------------------------------------------------------------------------------
[2023-03-15 14:07:50,995] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3635/tc_result.tsv
[2023-03-15 14:07:50,996] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:07:50,996] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:07:50,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg524f74a5-3fa9-4538-adf8-1342a5df2df7/dqc_reference/checkm_data
[2023-03-15 14:07:50,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:07:51,166] [INFO] Task started: CheckM
[2023-03-15 14:07:51,166] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3635/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3635/checkm_input OceanDNA-b3635/checkm_result
[2023-03-15 14:10:34,472] [INFO] Task succeeded: CheckM
[2023-03-15 14:10:34,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:10:34,515] [INFO] ===== Completeness check finished =====
[2023-03-15 14:10:34,515] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:10:34,516] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3635/markers.fasta)
[2023-03-15 14:10:34,517] [INFO] Task started: Blastn
[2023-03-15 14:10:34,517] [INFO] Running command: blastn -query OceanDNA-b3635/markers.fasta -db /var/lib/cwl/stg524f74a5-3fa9-4538-adf8-1342a5df2df7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3635/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:10:35,490] [INFO] Task succeeded: Blastn
[2023-03-15 14:10:35,493] [INFO] Selected 28 target genomes.
[2023-03-15 14:10:35,493] [INFO] Target genome list was writen to OceanDNA-b3635/target_genomes_gtdb.txt
[2023-03-15 14:10:35,532] [INFO] Task started: fastANI
[2023-03-15 14:10:35,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f20154f-a688-4efa-8036-7b935acdaaac/OceanDNA-b3635.fa --refList OceanDNA-b3635/target_genomes_gtdb.txt --output OceanDNA-b3635/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:10:57,960] [INFO] Task succeeded: fastANI
[2023-03-15 14:10:57,964] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:10:57,964] [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_009908745.1	s__Phaeodactylibacter sp009908745	75.6056	52	2851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Phaeodactylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214355.1	s__DT-111 sp013214355	75.4899	58	2851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__DT-111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715405.1	s__JABWBR01 sp016715405	75.2016	57	2851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JABWBR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360405.1	s__JABWBR01 sp013360405	75.07	57	2851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JABWBR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013299105.1	s__Haliscomenobacter sp013299105	75.0478	57	2851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Haliscomenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:10:57,966] [INFO] GTDB search result was written to OceanDNA-b3635/result_gtdb.tsv
[2023-03-15 14:10:57,970] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:10:57,975] [INFO] DFAST_QC result json was written to OceanDNA-b3635/dqc_result.json
[2023-03-15 14:10:57,975] [INFO] DFAST_QC completed!
[2023-03-15 14:10:57,975] [INFO] Total running time: 0h4m47s