[2023-03-17 00:02:20,726] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:02:20,726] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:02:20,726] [INFO] DQC Reference Directory: /var/lib/cwl/stg586b3c25-a9aa-4a66-8dda-0e20c9b839f0/dqc_reference
[2023-03-17 00:02:21,846] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:02:21,846] [INFO] Task started: Prodigal
[2023-03-17 00:02:21,846] [INFO] Running command: cat /var/lib/cwl/stg221703df-0221-4b34-9822-3cbffc2e95a8/OceanDNA-b45416.fa | prodigal -d OceanDNA-b45416/cds.fna -a OceanDNA-b45416/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:02:42,664] [INFO] Task succeeded: Prodigal
[2023-03-17 00:02:42,664] [INFO] Task started: HMMsearch
[2023-03-17 00:02:42,664] [INFO] Running command: hmmsearch --tblout OceanDNA-b45416/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg586b3c25-a9aa-4a66-8dda-0e20c9b839f0/dqc_reference/reference_markers.hmm OceanDNA-b45416/protein.faa > /dev/null
[2023-03-17 00:02:42,846] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:02:42,847] [INFO] Found 6/6 markers.
[2023-03-17 00:02:42,862] [INFO] Query marker FASTA was written to OceanDNA-b45416/markers.fasta
[2023-03-17 00:02:42,863] [INFO] Task started: Blastn
[2023-03-17 00:02:42,863] [INFO] Running command: blastn -query OceanDNA-b45416/markers.fasta -db /var/lib/cwl/stg586b3c25-a9aa-4a66-8dda-0e20c9b839f0/dqc_reference/reference_markers.fasta -out OceanDNA-b45416/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:02:43,408] [INFO] Task succeeded: Blastn
[2023-03-17 00:02:43,409] [INFO] Selected 19 target genomes.
[2023-03-17 00:02:43,409] [INFO] Target genome list was writen to OceanDNA-b45416/target_genomes.txt
[2023-03-17 00:02:43,488] [INFO] Task started: fastANI
[2023-03-17 00:02:43,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg221703df-0221-4b34-9822-3cbffc2e95a8/OceanDNA-b45416.fa --refList OceanDNA-b45416/target_genomes.txt --output OceanDNA-b45416/fastani_result.tsv --threads 1
[2023-03-17 00:02:59,881] [INFO] Task succeeded: fastANI
[2023-03-17 00:02:59,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg586b3c25-a9aa-4a66-8dda-0e20c9b839f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:02:59,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg586b3c25-a9aa-4a66-8dda-0e20c9b839f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:02:59,886] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:02:59,887] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:02:59,887] [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
Terrimicrobium sacchariphilum	strain=NM-5	GCA_001613545.1	690879	690879	type	True	76.9239	81	755	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	76.2207	65	755	95	below_threshold
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	76.1132	67	755	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:02:59,887] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45416/tc_result.tsv
[2023-03-17 00:02:59,887] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:02:59,887] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:02:59,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg586b3c25-a9aa-4a66-8dda-0e20c9b839f0/dqc_reference/checkm_data
[2023-03-17 00:02:59,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:02:59,946] [INFO] Task started: CheckM
[2023-03-17 00:02:59,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45416/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45416/checkm_input OceanDNA-b45416/checkm_result
[2023-03-17 00:03:53,577] [INFO] Task succeeded: CheckM
[2023-03-17 00:03:53,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:03:53,599] [INFO] ===== Completeness check finished =====
[2023-03-17 00:03:53,599] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:03:53,600] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45416/markers.fasta)
[2023-03-17 00:03:53,601] [INFO] Task started: Blastn
[2023-03-17 00:03:53,601] [INFO] Running command: blastn -query OceanDNA-b45416/markers.fasta -db /var/lib/cwl/stg586b3c25-a9aa-4a66-8dda-0e20c9b839f0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45416/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:03:54,464] [INFO] Task succeeded: Blastn
[2023-03-17 00:03:54,483] [INFO] Selected 12 target genomes.
[2023-03-17 00:03:54,483] [INFO] Target genome list was writen to OceanDNA-b45416/target_genomes_gtdb.txt
[2023-03-17 00:03:54,538] [INFO] Task started: fastANI
[2023-03-17 00:03:54,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg221703df-0221-4b34-9822-3cbffc2e95a8/OceanDNA-b45416.fa --refList OceanDNA-b45416/target_genomes_gtdb.txt --output OceanDNA-b45416/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:04:00,538] [INFO] Task succeeded: fastANI
[2023-03-17 00:04:00,544] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:04:00,544] [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_018970255.1	s__UBA967 sp018970255	79.5198	280	755	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402345.1	s__UBA967 sp018402345	79.3604	295	755	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903915315.1	s__UBA967 sp903915315	78.5486	118	755	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002396485.1	s__UBA967 sp002396485	78.4919	214	755	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886045.1	s__UBA967 sp009886045	78.364	162	755	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920585.1	s__UBA967 sp009920585	78.1224	126	755	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	99.04	99.04	0.77	0.77	2	-
GCA_002290555.1	s__UBA967 sp002290555	77.9316	146	755	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	99.67	99.67	0.84	0.84	2	-
GCA_007280915.1	s__QYQL01 sp007280915	76.9408	109	755	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__QYQL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879575.1	s__QYQL01 sp014879575	76.3524	70	755	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__QYQL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:04:00,557] [INFO] GTDB search result was written to OceanDNA-b45416/result_gtdb.tsv
[2023-03-17 00:04:00,558] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:04:00,559] [INFO] DFAST_QC result json was written to OceanDNA-b45416/dqc_result.json
[2023-03-17 00:04:00,559] [INFO] DFAST_QC completed!
[2023-03-17 00:04:00,559] [INFO] Total running time: 0h1m40s