[2023-03-19 03:28:07,303] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:28:07,303] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:28:07,303] [INFO] DQC Reference Directory: /var/lib/cwl/stga02fcb0c-21d4-4e03-abeb-c8452a16d924/dqc_reference
[2023-03-19 03:28:08,404] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:28:08,404] [INFO] Task started: Prodigal
[2023-03-19 03:28:08,404] [INFO] Running command: cat /var/lib/cwl/stgaff523b8-9e0f-4dc7-b8db-0765d709e09d/OceanDNA-b14460.fa | prodigal -d OceanDNA-b14460/cds.fna -a OceanDNA-b14460/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:28:13,192] [INFO] Task succeeded: Prodigal
[2023-03-19 03:28:13,192] [INFO] Task started: HMMsearch
[2023-03-19 03:28:13,192] [INFO] Running command: hmmsearch --tblout OceanDNA-b14460/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga02fcb0c-21d4-4e03-abeb-c8452a16d924/dqc_reference/reference_markers.hmm OceanDNA-b14460/protein.faa > /dev/null
[2023-03-19 03:28:13,329] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:28:13,330] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaff523b8-9e0f-4dc7-b8db-0765d709e09d/OceanDNA-b14460.fa]
[2023-03-19 03:28:13,339] [INFO] Query marker FASTA was written to OceanDNA-b14460/markers.fasta
[2023-03-19 03:28:13,339] [INFO] Task started: Blastn
[2023-03-19 03:28:13,339] [INFO] Running command: blastn -query OceanDNA-b14460/markers.fasta -db /var/lib/cwl/stga02fcb0c-21d4-4e03-abeb-c8452a16d924/dqc_reference/reference_markers.fasta -out OceanDNA-b14460/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:28:13,767] [INFO] Task succeeded: Blastn
[2023-03-19 03:28:13,768] [INFO] Selected 13 target genomes.
[2023-03-19 03:28:13,768] [INFO] Target genome list was writen to OceanDNA-b14460/target_genomes.txt
[2023-03-19 03:28:13,778] [INFO] Task started: fastANI
[2023-03-19 03:28:13,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgaff523b8-9e0f-4dc7-b8db-0765d709e09d/OceanDNA-b14460.fa --refList OceanDNA-b14460/target_genomes.txt --output OceanDNA-b14460/fastani_result.tsv --threads 1
[2023-03-19 03:28:19,016] [INFO] Task succeeded: fastANI
[2023-03-19 03:28:19,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga02fcb0c-21d4-4e03-abeb-c8452a16d924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:28:19,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga02fcb0c-21d4-4e03-abeb-c8452a16d924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:28:19,016] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:28:19,017] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:28:19,017] [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
--------------------------------------------------------------------------------
[2023-03-19 03:28:19,017] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14460/tc_result.tsv
[2023-03-19 03:28:19,017] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:28:19,017] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:28:19,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga02fcb0c-21d4-4e03-abeb-c8452a16d924/dqc_reference/checkm_data
[2023-03-19 03:28:19,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:28:19,022] [INFO] Task started: CheckM
[2023-03-19 03:28:19,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14460/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14460/checkm_input OceanDNA-b14460/checkm_result
[2023-03-19 03:28:36,839] [INFO] Task succeeded: CheckM
[2023-03-19 03:28:36,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:28:36,841] [INFO] ===== Completeness check finished =====
[2023-03-19 03:28:36,841] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:28:36,841] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14460/markers.fasta)
[2023-03-19 03:28:36,841] [INFO] Task started: Blastn
[2023-03-19 03:28:36,841] [INFO] Running command: blastn -query OceanDNA-b14460/markers.fasta -db /var/lib/cwl/stga02fcb0c-21d4-4e03-abeb-c8452a16d924/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14460/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:28:37,266] [INFO] Task succeeded: Blastn
[2023-03-19 03:28:37,267] [INFO] Selected 7 target genomes.
[2023-03-19 03:28:37,267] [INFO] Target genome list was writen to OceanDNA-b14460/target_genomes_gtdb.txt
[2023-03-19 03:28:37,274] [INFO] Task started: fastANI
[2023-03-19 03:28:37,274] [INFO] Running command: fastANI --query /var/lib/cwl/stgaff523b8-9e0f-4dc7-b8db-0765d709e09d/OceanDNA-b14460.fa --refList OceanDNA-b14460/target_genomes_gtdb.txt --output OceanDNA-b14460/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:28:39,062] [INFO] Task succeeded: fastANI
[2023-03-19 03:28:39,066] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:28:39,066] [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_002728715.1	s__GCA-002708145 sp002728715	97.7678	298	318	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002708145	95.0	98.77	97.83	0.89	0.87	3	conclusive
GCA_002714425.1	s__GCA-002708145 sp002714425	92.1468	315	318	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002708145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712125.1	s__GCA-002708145 sp002712125	88.0409	280	318	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002708145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708145.1	s__GCA-002708145 sp002708145	82.2456	229	318	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002708145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:28:39,066] [INFO] GTDB search result was written to OceanDNA-b14460/result_gtdb.tsv
[2023-03-19 03:28:39,066] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:28:39,067] [INFO] DFAST_QC result json was written to OceanDNA-b14460/dqc_result.json
[2023-03-19 03:28:39,067] [INFO] DFAST_QC completed!
[2023-03-19 03:28:39,067] [INFO] Total running time: 0h0m32s