[2023-03-18 02:42:32,854] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:42:32,854] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:42:32,854] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1f1dca3-c048-48d9-aea3-ac8de1aff624/dqc_reference
[2023-03-18 02:42:34,115] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:42:34,116] [INFO] Task started: Prodigal
[2023-03-18 02:42:34,117] [INFO] Running command: cat /var/lib/cwl/stgfa7f60fd-0162-4eb1-a0a1-51d744b8b964/OceanDNA-b44705.fa | prodigal -d OceanDNA-b44705/cds.fna -a OceanDNA-b44705/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:42:42,503] [INFO] Task succeeded: Prodigal
[2023-03-18 02:42:42,504] [INFO] Task started: HMMsearch
[2023-03-18 02:42:42,504] [INFO] Running command: hmmsearch --tblout OceanDNA-b44705/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1f1dca3-c048-48d9-aea3-ac8de1aff624/dqc_reference/reference_markers.hmm OceanDNA-b44705/protein.faa > /dev/null
[2023-03-18 02:42:42,668] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:42:42,669] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfa7f60fd-0162-4eb1-a0a1-51d744b8b964/OceanDNA-b44705.fa]
[2023-03-18 02:42:42,683] [INFO] Query marker FASTA was written to OceanDNA-b44705/markers.fasta
[2023-03-18 02:42:42,683] [INFO] Task started: Blastn
[2023-03-18 02:42:42,683] [INFO] Running command: blastn -query OceanDNA-b44705/markers.fasta -db /var/lib/cwl/stgf1f1dca3-c048-48d9-aea3-ac8de1aff624/dqc_reference/reference_markers.fasta -out OceanDNA-b44705/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:42:43,222] [INFO] Task succeeded: Blastn
[2023-03-18 02:42:43,223] [INFO] Selected 11 target genomes.
[2023-03-18 02:42:43,223] [INFO] Target genome list was writen to OceanDNA-b44705/target_genomes.txt
[2023-03-18 02:42:43,228] [INFO] Task started: fastANI
[2023-03-18 02:42:43,228] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa7f60fd-0162-4eb1-a0a1-51d744b8b964/OceanDNA-b44705.fa --refList OceanDNA-b44705/target_genomes.txt --output OceanDNA-b44705/fastani_result.tsv --threads 1
[2023-03-18 02:42:49,132] [INFO] Task succeeded: fastANI
[2023-03-18 02:42:49,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1f1dca3-c048-48d9-aea3-ac8de1aff624/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:42:49,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1f1dca3-c048-48d9-aea3-ac8de1aff624/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:42:49,132] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:42:49,133] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:42:49,133] [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 02:42:49,133] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44705/tc_result.tsv
[2023-03-18 02:42:49,133] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:42:49,133] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:42:49,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1f1dca3-c048-48d9-aea3-ac8de1aff624/dqc_reference/checkm_data
[2023-03-18 02:42:49,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:42:49,139] [INFO] Task started: CheckM
[2023-03-18 02:42:49,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44705/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44705/checkm_input OceanDNA-b44705/checkm_result
[2023-03-18 02:43:15,217] [INFO] Task succeeded: CheckM
[2023-03-18 02:43:15,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:43:15,220] [INFO] ===== Completeness check finished =====
[2023-03-18 02:43:15,220] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:43:15,220] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44705/markers.fasta)
[2023-03-18 02:43:15,220] [INFO] Task started: Blastn
[2023-03-18 02:43:15,220] [INFO] Running command: blastn -query OceanDNA-b44705/markers.fasta -db /var/lib/cwl/stgf1f1dca3-c048-48d9-aea3-ac8de1aff624/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44705/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:43:16,083] [INFO] Task succeeded: Blastn
[2023-03-18 02:43:16,084] [INFO] Selected 27 target genomes.
[2023-03-18 02:43:16,084] [INFO] Target genome list was writen to OceanDNA-b44705/target_genomes_gtdb.txt
[2023-03-18 02:43:16,357] [INFO] Task started: fastANI
[2023-03-18 02:43:16,357] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa7f60fd-0162-4eb1-a0a1-51d744b8b964/OceanDNA-b44705.fa --refList OceanDNA-b44705/target_genomes_gtdb.txt --output OceanDNA-b44705/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:43:26,436] [INFO] Task succeeded: fastANI
[2023-03-18 02:43:26,438] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:43:26,438] [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_902575715.1	s__Arctic96AD-7 sp902575715	93.3197	144	331	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902590435.1	s__Arctic96AD-7 sp902590435	77.276	89	331	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:43:26,438] [INFO] GTDB search result was written to OceanDNA-b44705/result_gtdb.tsv
[2023-03-18 02:43:26,439] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:43:26,439] [INFO] DFAST_QC result json was written to OceanDNA-b44705/dqc_result.json
[2023-03-18 02:43:26,439] [INFO] DFAST_QC completed!
[2023-03-18 02:43:26,439] [INFO] Total running time: 0h0m54s