[2023-03-18 09:15:00,470] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:15:00,470] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:15:00,470] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7bc3023-1bed-469f-930c-4e95e40a6b54/dqc_reference
[2023-03-18 09:15:02,030] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:15:02,030] [INFO] Task started: Prodigal
[2023-03-18 09:15:02,030] [INFO] Running command: cat /var/lib/cwl/stg77d29a83-d616-4c00-9a3f-33365aebf8a7/OceanDNA-b17353.fa | prodigal -d OceanDNA-b17353/cds.fna -a OceanDNA-b17353/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:15:14,464] [INFO] Task succeeded: Prodigal
[2023-03-18 09:15:14,464] [INFO] Task started: HMMsearch
[2023-03-18 09:15:14,464] [INFO] Running command: hmmsearch --tblout OceanDNA-b17353/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7bc3023-1bed-469f-930c-4e95e40a6b54/dqc_reference/reference_markers.hmm OceanDNA-b17353/protein.faa > /dev/null
[2023-03-18 09:15:14,654] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:15:14,654] [INFO] Found 6/6 markers.
[2023-03-18 09:15:14,691] [INFO] Query marker FASTA was written to OceanDNA-b17353/markers.fasta
[2023-03-18 09:15:14,692] [INFO] Task started: Blastn
[2023-03-18 09:15:14,693] [INFO] Running command: blastn -query OceanDNA-b17353/markers.fasta -db /var/lib/cwl/stgc7bc3023-1bed-469f-930c-4e95e40a6b54/dqc_reference/reference_markers.fasta -out OceanDNA-b17353/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:15,221] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:15,227] [INFO] Selected 16 target genomes.
[2023-03-18 09:15:15,227] [INFO] Target genome list was writen to OceanDNA-b17353/target_genomes.txt
[2023-03-18 09:15:15,236] [INFO] Task started: fastANI
[2023-03-18 09:15:15,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg77d29a83-d616-4c00-9a3f-33365aebf8a7/OceanDNA-b17353.fa --refList OceanDNA-b17353/target_genomes.txt --output OceanDNA-b17353/fastani_result.tsv --threads 1
[2023-03-18 09:15:24,484] [INFO] Task succeeded: fastANI
[2023-03-18 09:15:24,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7bc3023-1bed-469f-930c-4e95e40a6b54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:15:24,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7bc3023-1bed-469f-930c-4e95e40a6b54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:15:24,484] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:15:24,484] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:15:24,485] [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 09:15:24,486] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17353/tc_result.tsv
[2023-03-18 09:15:24,486] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:15:24,486] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:15:24,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7bc3023-1bed-469f-930c-4e95e40a6b54/dqc_reference/checkm_data
[2023-03-18 09:15:24,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:15:24,495] [INFO] Task started: CheckM
[2023-03-18 09:15:24,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17353/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17353/checkm_input OceanDNA-b17353/checkm_result
[2023-03-18 09:15:58,079] [INFO] Task succeeded: CheckM
[2023-03-18 09:15:58,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:15:58,081] [INFO] ===== Completeness check finished =====
[2023-03-18 09:15:58,082] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:15:58,082] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17353/markers.fasta)
[2023-03-18 09:15:58,083] [INFO] Task started: Blastn
[2023-03-18 09:15:58,083] [INFO] Running command: blastn -query OceanDNA-b17353/markers.fasta -db /var/lib/cwl/stgc7bc3023-1bed-469f-930c-4e95e40a6b54/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17353/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:58,797] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:58,798] [INFO] Selected 13 target genomes.
[2023-03-18 09:15:58,798] [INFO] Target genome list was writen to OceanDNA-b17353/target_genomes_gtdb.txt
[2023-03-18 09:15:58,814] [INFO] Task started: fastANI
[2023-03-18 09:15:58,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg77d29a83-d616-4c00-9a3f-33365aebf8a7/OceanDNA-b17353.fa --refList OceanDNA-b17353/target_genomes_gtdb.txt --output OceanDNA-b17353/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:16:04,600] [INFO] Task succeeded: fastANI
[2023-03-18 09:16:04,604] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:16:04,604] [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_002500925.1	s__UBA2589 sp002500925	98.8592	600	672	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.15	98.29	0.89	0.88	10	conclusive
GCA_002348465.1	s__UBA2589 sp002348465	91.9335	561	672	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	98.53	97.69	0.86	0.81	4	-
GCA_002348265.1	s__UBA2589 sp002348265	91.4839	590	672	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.66	99.56	0.93	0.92	5	-
GCA_002390225.1	s__UBA2589 sp002390225	76.7829	69	672	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:16:04,604] [INFO] GTDB search result was written to OceanDNA-b17353/result_gtdb.tsv
[2023-03-18 09:16:04,604] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:16:04,605] [INFO] DFAST_QC result json was written to OceanDNA-b17353/dqc_result.json
[2023-03-18 09:16:04,605] [INFO] DFAST_QC completed!
[2023-03-18 09:16:04,605] [INFO] Total running time: 0h1m4s