[2023-03-16 08:59:43,909] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:59:43,909] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:59:43,909] [INFO] DQC Reference Directory: /var/lib/cwl/stgcca8d88c-eed4-49c3-a18f-67c7c2a27428/dqc_reference
[2023-03-16 08:59:45,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:59:45,387] [INFO] Task started: Prodigal
[2023-03-16 08:59:45,387] [INFO] Running command: cat /var/lib/cwl/stg1ac9141c-67d9-43c4-bf46-d2d62bcad2b7/OceanDNA-b45287.fa | prodigal -d OceanDNA-b45287/cds.fna -a OceanDNA-b45287/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:00:02,269] [INFO] Task succeeded: Prodigal
[2023-03-16 09:00:02,269] [INFO] Task started: HMMsearch
[2023-03-16 09:00:02,269] [INFO] Running command: hmmsearch --tblout OceanDNA-b45287/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcca8d88c-eed4-49c3-a18f-67c7c2a27428/dqc_reference/reference_markers.hmm OceanDNA-b45287/protein.faa > /dev/null
[2023-03-16 09:00:02,469] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:00:02,469] [INFO] Found 6/6 markers.
[2023-03-16 09:00:02,492] [INFO] Query marker FASTA was written to OceanDNA-b45287/markers.fasta
[2023-03-16 09:00:02,493] [INFO] Task started: Blastn
[2023-03-16 09:00:02,494] [INFO] Running command: blastn -query OceanDNA-b45287/markers.fasta -db /var/lib/cwl/stgcca8d88c-eed4-49c3-a18f-67c7c2a27428/dqc_reference/reference_markers.fasta -out OceanDNA-b45287/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:00:03,071] [INFO] Task succeeded: Blastn
[2023-03-16 09:00:03,072] [INFO] Selected 30 target genomes.
[2023-03-16 09:00:03,072] [INFO] Target genome list was writen to OceanDNA-b45287/target_genomes.txt
[2023-03-16 09:00:03,087] [INFO] Task started: fastANI
[2023-03-16 09:00:03,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ac9141c-67d9-43c4-bf46-d2d62bcad2b7/OceanDNA-b45287.fa --refList OceanDNA-b45287/target_genomes.txt --output OceanDNA-b45287/fastani_result.tsv --threads 1
[2023-03-16 09:00:20,711] [INFO] Task succeeded: fastANI
[2023-03-16 09:00:20,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcca8d88c-eed4-49c3-a18f-67c7c2a27428/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:00:20,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcca8d88c-eed4-49c3-a18f-67c7c2a27428/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:00:20,712] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:00:20,712] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:00:20,712] [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 09:00:20,713] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45287/tc_result.tsv
[2023-03-16 09:00:20,713] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:00:20,713] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:00:20,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcca8d88c-eed4-49c3-a18f-67c7c2a27428/dqc_reference/checkm_data
[2023-03-16 09:00:20,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:00:20,721] [INFO] Task started: CheckM
[2023-03-16 09:00:20,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45287/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45287/checkm_input OceanDNA-b45287/checkm_result
[2023-03-16 09:01:04,708] [INFO] Task succeeded: CheckM
[2023-03-16 09:01:04,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:01:04,783] [INFO] ===== Completeness check finished =====
[2023-03-16 09:01:04,783] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:01:04,783] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45287/markers.fasta)
[2023-03-16 09:01:04,784] [INFO] Task started: Blastn
[2023-03-16 09:01:04,784] [INFO] Running command: blastn -query OceanDNA-b45287/markers.fasta -db /var/lib/cwl/stgcca8d88c-eed4-49c3-a18f-67c7c2a27428/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45287/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:01:05,707] [INFO] Task succeeded: Blastn
[2023-03-16 09:01:05,708] [INFO] Selected 28 target genomes.
[2023-03-16 09:01:05,708] [INFO] Target genome list was writen to OceanDNA-b45287/target_genomes_gtdb.txt
[2023-03-16 09:01:05,735] [INFO] Task started: fastANI
[2023-03-16 09:01:05,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ac9141c-67d9-43c4-bf46-d2d62bcad2b7/OceanDNA-b45287.fa --refList OceanDNA-b45287/target_genomes_gtdb.txt --output OceanDNA-b45287/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:01:22,742] [INFO] Task succeeded: fastANI
[2023-03-16 09:01:22,746] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:01:22,747] [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_001790955.1	s__2-12-FULL-69-37 sp001790955	77.2434	180	916	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__2-12-FULL-69-37	95.0	99.54	99.54	0.87	0.87	2	-
GCA_016192135.1	s__2-12-FULL-69-37 sp016192135	77.1348	201	916	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__2-12-FULL-69-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016184445.1	s__2-12-FULL-69-37 sp016184445	77.1019	105	916	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__2-12-FULL-69-37	95.0	97.02	97.02	0.69	0.69	2	-
GCA_002238965.1	s__Bin107 sp002238965	76.7012	120	916	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__Bin107	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009839615.1	s__Bin107 sp009839615	76.5324	128	916	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__Bin107	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523725.1	s__Bin107 sp011523725	76.4498	125	916	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__Bin107	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:01:22,747] [INFO] GTDB search result was written to OceanDNA-b45287/result_gtdb.tsv
[2023-03-16 09:01:22,747] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:01:22,748] [INFO] DFAST_QC result json was written to OceanDNA-b45287/dqc_result.json
[2023-03-16 09:01:22,748] [INFO] DFAST_QC completed!
[2023-03-16 09:01:22,748] [INFO] Total running time: 0h1m39s