[2023-03-17 00:45:47,188] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,189] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,189] [INFO] DQC Reference Directory: /var/lib/cwl/stgad9831ed-444e-4861-8dda-0009e7760128/dqc_reference
[2023-03-17 00:45:48,351] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,352] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,353] [INFO] Running command: cat /var/lib/cwl/stg8c00e4a5-2dbb-48b9-911a-2c21feefe842/OceanDNA-b30786.fa | prodigal -d OceanDNA-b30786/cds.fna -a OceanDNA-b30786/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:45:56,003] [INFO] Task succeeded: Prodigal
[2023-03-17 00:45:56,003] [INFO] Task started: HMMsearch
[2023-03-17 00:45:56,003] [INFO] Running command: hmmsearch --tblout OceanDNA-b30786/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad9831ed-444e-4861-8dda-0009e7760128/dqc_reference/reference_markers.hmm OceanDNA-b30786/protein.faa > /dev/null
[2023-03-17 00:45:56,156] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:45:56,156] [INFO] Found 6/6 markers.
[2023-03-17 00:45:56,172] [INFO] Query marker FASTA was written to OceanDNA-b30786/markers.fasta
[2023-03-17 00:45:56,173] [INFO] Task started: Blastn
[2023-03-17 00:45:56,173] [INFO] Running command: blastn -query OceanDNA-b30786/markers.fasta -db /var/lib/cwl/stgad9831ed-444e-4861-8dda-0009e7760128/dqc_reference/reference_markers.fasta -out OceanDNA-b30786/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:45:56,852] [INFO] Task succeeded: Blastn
[2023-03-17 00:45:56,853] [INFO] Selected 33 target genomes.
[2023-03-17 00:45:56,854] [INFO] Target genome list was writen to OceanDNA-b30786/target_genomes.txt
[2023-03-17 00:45:56,935] [INFO] Task started: fastANI
[2023-03-17 00:45:56,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c00e4a5-2dbb-48b9-911a-2c21feefe842/OceanDNA-b30786.fa --refList OceanDNA-b30786/target_genomes.txt --output OceanDNA-b30786/fastani_result.tsv --threads 1
[2023-03-17 00:46:20,715] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:20,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad9831ed-444e-4861-8dda-0009e7760128/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:20,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad9831ed-444e-4861-8dda-0009e7760128/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:20,716] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:20,716] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:46:20,716] [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
--------------------------------------------------------------------------------
[2023-03-17 00:46:20,718] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30786/tc_result.tsv
[2023-03-17 00:46:20,718] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:20,718] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:20,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad9831ed-444e-4861-8dda-0009e7760128/dqc_reference/checkm_data
[2023-03-17 00:46:20,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:20,725] [INFO] Task started: CheckM
[2023-03-17 00:46:20,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30786/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30786/checkm_input OceanDNA-b30786/checkm_result
[2023-03-17 00:46:45,259] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:45,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.41%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:45,261] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:45,262] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:45,262] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30786/markers.fasta)
[2023-03-17 00:46:45,262] [INFO] Task started: Blastn
[2023-03-17 00:46:45,262] [INFO] Running command: blastn -query OceanDNA-b30786/markers.fasta -db /var/lib/cwl/stgad9831ed-444e-4861-8dda-0009e7760128/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30786/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:46,534] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:46,535] [INFO] Selected 16 target genomes.
[2023-03-17 00:46:46,535] [INFO] Target genome list was writen to OceanDNA-b30786/target_genomes_gtdb.txt
[2023-03-17 00:46:46,897] [INFO] Task started: fastANI
[2023-03-17 00:46:46,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c00e4a5-2dbb-48b9-911a-2c21feefe842/OceanDNA-b30786.fa --refList OceanDNA-b30786/target_genomes_gtdb.txt --output OceanDNA-b30786/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:46:54,876] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:54,881] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:46:54,881] [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_002938315.1	s__Casp-alpha2 sp002938315	86.9328	262	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.33	99.24	0.87	0.79	4	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	78.9249	150	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	78.7835	153	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	78.4179	110	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCA_013203955.1	s__Casp-alpha2 sp013203955	78.31	128	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763915.1	s__Casp-alpha2 sp016763915	78.2405	88	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510075.1	s__Casp-alpha2 sp001510075	78.1482	88	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204265.1	s__Casp-alpha2 sp013204265	78.0883	126	330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:46:54,882] [INFO] GTDB search result was written to OceanDNA-b30786/result_gtdb.tsv
[2023-03-17 00:46:54,882] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:46:54,882] [INFO] DFAST_QC result json was written to OceanDNA-b30786/dqc_result.json
[2023-03-17 00:46:54,883] [INFO] DFAST_QC completed!
[2023-03-17 00:46:54,883] [INFO] Total running time: 0h1m8s