[2023-03-16 04:38:30,088] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:38:30,089] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:38:30,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e173d1b-64f2-46da-8287-5748dcd51400/dqc_reference
[2023-03-16 04:38:31,195] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:38:31,195] [INFO] Task started: Prodigal
[2023-03-16 04:38:31,195] [INFO] Running command: cat /var/lib/cwl/stg53bcd92d-ddf5-4b3d-89d2-8cdad0a0201e/OceanDNA-b14750.fa | prodigal -d OceanDNA-b14750/cds.fna -a OceanDNA-b14750/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:38:35,142] [INFO] Task succeeded: Prodigal
[2023-03-16 04:38:35,142] [INFO] Task started: HMMsearch
[2023-03-16 04:38:35,142] [INFO] Running command: hmmsearch --tblout OceanDNA-b14750/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e173d1b-64f2-46da-8287-5748dcd51400/dqc_reference/reference_markers.hmm OceanDNA-b14750/protein.faa > /dev/null
[2023-03-16 04:38:35,280] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:38:35,281] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg53bcd92d-ddf5-4b3d-89d2-8cdad0a0201e/OceanDNA-b14750.fa]
[2023-03-16 04:38:35,289] [INFO] Query marker FASTA was written to OceanDNA-b14750/markers.fasta
[2023-03-16 04:38:35,291] [INFO] Task started: Blastn
[2023-03-16 04:38:35,291] [INFO] Running command: blastn -query OceanDNA-b14750/markers.fasta -db /var/lib/cwl/stg8e173d1b-64f2-46da-8287-5748dcd51400/dqc_reference/reference_markers.fasta -out OceanDNA-b14750/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:38:35,831] [INFO] Task succeeded: Blastn
[2023-03-16 04:38:35,832] [INFO] Selected 18 target genomes.
[2023-03-16 04:38:35,832] [INFO] Target genome list was writen to OceanDNA-b14750/target_genomes.txt
[2023-03-16 04:38:35,843] [INFO] Task started: fastANI
[2023-03-16 04:38:35,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg53bcd92d-ddf5-4b3d-89d2-8cdad0a0201e/OceanDNA-b14750.fa --refList OceanDNA-b14750/target_genomes.txt --output OceanDNA-b14750/fastani_result.tsv --threads 1
[2023-03-16 04:38:44,101] [INFO] Task succeeded: fastANI
[2023-03-16 04:38:44,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e173d1b-64f2-46da-8287-5748dcd51400/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:38:44,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e173d1b-64f2-46da-8287-5748dcd51400/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:38:44,102] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:38:44,102] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:38:44,102] [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
--------------------------------------------------------------------------------
[2023-03-16 04:38:44,102] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14750/tc_result.tsv
[2023-03-16 04:38:44,102] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:38:44,102] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:38:44,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e173d1b-64f2-46da-8287-5748dcd51400/dqc_reference/checkm_data
[2023-03-16 04:38:44,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:38:44,108] [INFO] Task started: CheckM
[2023-03-16 04:38:44,108] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14750/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14750/checkm_input OceanDNA-b14750/checkm_result
[2023-03-16 04:39:02,310] [INFO] Task succeeded: CheckM
[2023-03-16 04:39:02,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.89%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:39:02,312] [INFO] ===== Completeness check finished =====
[2023-03-16 04:39:02,312] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:39:02,312] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14750/markers.fasta)
[2023-03-16 04:39:02,314] [INFO] Task started: Blastn
[2023-03-16 04:39:02,314] [INFO] Running command: blastn -query OceanDNA-b14750/markers.fasta -db /var/lib/cwl/stg8e173d1b-64f2-46da-8287-5748dcd51400/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14750/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:39:03,131] [INFO] Task succeeded: Blastn
[2023-03-16 04:39:03,132] [INFO] Selected 13 target genomes.
[2023-03-16 04:39:03,132] [INFO] Target genome list was writen to OceanDNA-b14750/target_genomes_gtdb.txt
[2023-03-16 04:39:03,140] [INFO] Task started: fastANI
[2023-03-16 04:39:03,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg53bcd92d-ddf5-4b3d-89d2-8cdad0a0201e/OceanDNA-b14750.fa --refList OceanDNA-b14750/target_genomes_gtdb.txt --output OceanDNA-b14750/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:39:06,908] [INFO] Task succeeded: fastANI
[2023-03-16 04:39:06,911] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:39:06,911] [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_002727435.1	s__GCA-002700125 sp002727435	97.9964	130	225	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902620405.1	s__GCA-002700125 sp902620405	92.3376	158	225	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911545.1	s__GCA-002700125 sp013911545	78.536	87	225	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:39:06,911] [INFO] GTDB search result was written to OceanDNA-b14750/result_gtdb.tsv
[2023-03-16 04:39:06,912] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:39:06,912] [INFO] DFAST_QC result json was written to OceanDNA-b14750/dqc_result.json
[2023-03-16 04:39:06,912] [INFO] DFAST_QC completed!
[2023-03-16 04:39:06,912] [INFO] Total running time: 0h0m37s