[2023-03-16 17:25:08,951] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:25:08,951] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:25:08,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg28d0b383-3d5b-4bae-8613-4d5c808a90de/dqc_reference
[2023-03-16 17:25:10,173] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:25:10,173] [INFO] Task started: Prodigal
[2023-03-16 17:25:10,173] [INFO] Running command: cat /var/lib/cwl/stg65e83bab-fb5a-4ae4-b490-71e9082606af/OceanDNA-b47088.fa | prodigal -d OceanDNA-b47088/cds.fna -a OceanDNA-b47088/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:26:18,116] [INFO] Task succeeded: Prodigal
[2023-03-16 17:26:18,116] [INFO] Task started: HMMsearch
[2023-03-16 17:26:18,116] [INFO] Running command: hmmsearch --tblout OceanDNA-b47088/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28d0b383-3d5b-4bae-8613-4d5c808a90de/dqc_reference/reference_markers.hmm OceanDNA-b47088/protein.faa > /dev/null
[2023-03-16 17:26:18,381] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:26:18,382] [INFO] Found 6/6 markers.
[2023-03-16 17:26:18,415] [INFO] Query marker FASTA was written to OceanDNA-b47088/markers.fasta
[2023-03-16 17:26:18,416] [INFO] Task started: Blastn
[2023-03-16 17:26:18,416] [INFO] Running command: blastn -query OceanDNA-b47088/markers.fasta -db /var/lib/cwl/stg28d0b383-3d5b-4bae-8613-4d5c808a90de/dqc_reference/reference_markers.fasta -out OceanDNA-b47088/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:26:18,972] [INFO] Task succeeded: Blastn
[2023-03-16 17:26:18,973] [INFO] Selected 20 target genomes.
[2023-03-16 17:26:18,973] [INFO] Target genome list was writen to OceanDNA-b47088/target_genomes.txt
[2023-03-16 17:26:18,986] [INFO] Task started: fastANI
[2023-03-16 17:26:18,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg65e83bab-fb5a-4ae4-b490-71e9082606af/OceanDNA-b47088.fa --refList OceanDNA-b47088/target_genomes.txt --output OceanDNA-b47088/fastani_result.tsv --threads 1
[2023-03-16 17:26:38,004] [INFO] Task succeeded: fastANI
[2023-03-16 17:26:38,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28d0b383-3d5b-4bae-8613-4d5c808a90de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:26:38,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28d0b383-3d5b-4bae-8613-4d5c808a90de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:26:38,012] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:26:38,012] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:26:38,012] [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
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	79.2458	813	1854	95	below_threshold
Brevifollis gellanilyticus	strain=NBRC 108608	GCA_007992435.1	748831	748831	type	True	77.6539	479	1854	95	below_threshold
Prosthecobacter fusiformis	strain=ATCC 25309	GCA_004364345.1	48464	48464	type	True	77.1628	245	1854	95	below_threshold
Prosthecobacter dejongeii	strain=DSM 12251	GCA_014203045.1	48465	48465	type	True	77.1096	251	1854	95	below_threshold
Prosthecobacter debontii	strain=ATCC 700200	GCA_900167535.1	48467	48467	type	True	77.0178	257	1854	95	below_threshold
Roseimicrobium gellanilyticum	strain=DSM 25532	GCA_003315205.1	748857	748857	type	True	76.8115	230	1854	95	below_threshold
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	76.6394	197	1854	95	below_threshold
Phragmitibacter flavus	strain=MG-N-17	GCA_005780165.1	2576071	2576071	type	True	76.2231	147	1854	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	75.9812	107	1854	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:26:38,012] [INFO] DFAST Taxonomy check result was written to OceanDNA-b47088/tc_result.tsv
[2023-03-16 17:26:38,013] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:26:38,013] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:26:38,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28d0b383-3d5b-4bae-8613-4d5c808a90de/dqc_reference/checkm_data
[2023-03-16 17:26:38,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:26:38,029] [INFO] Task started: CheckM
[2023-03-16 17:26:38,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b47088/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b47088/checkm_input OceanDNA-b47088/checkm_result
[2023-03-16 17:30:07,422] [INFO] Task succeeded: CheckM
[2023-03-16 17:30:07,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:30:07,428] [INFO] ===== Completeness check finished =====
[2023-03-16 17:30:07,429] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:30:07,429] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b47088/markers.fasta)
[2023-03-16 17:30:07,430] [INFO] Task started: Blastn
[2023-03-16 17:30:07,430] [INFO] Running command: blastn -query OceanDNA-b47088/markers.fasta -db /var/lib/cwl/stg28d0b383-3d5b-4bae-8613-4d5c808a90de/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b47088/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:30:08,478] [INFO] Task succeeded: Blastn
[2023-03-16 17:30:08,482] [INFO] Selected 12 target genomes.
[2023-03-16 17:30:08,482] [INFO] Target genome list was writen to OceanDNA-b47088/target_genomes_gtdb.txt
[2023-03-16 17:30:08,490] [INFO] Task started: fastANI
[2023-03-16 17:30:08,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg65e83bab-fb5a-4ae4-b490-71e9082606af/OceanDNA-b47088.fa --refList OceanDNA-b47088/target_genomes_gtdb.txt --output OceanDNA-b47088/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:30:24,342] [INFO] Task succeeded: fastANI
[2023-03-16 17:30:24,350] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:30:24,350] [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_003506995.1	s__Prosthecobacter sp003506995	81.4	888	1854	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795375.1	s__Prosthecobacter sp016795375	80.8441	764	1854	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879935.1	s__Prosthecobacter sp014879935	80.733	1031	1854	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848465.1	s__Prosthecobacter sp903848465	80.0348	760	1854	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	99.97	99.92	0.97	0.96	6	-
GCA_017301975.1	s__Prosthecobacter sp017301975	79.9484	873	1854	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075365.1	s__Prosthecobacter sp015075365	79.9233	841	1854	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279765.1	s__Prosthecobacter sp002279765	79.8871	826	1854	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795465.1	s__Prosthecobacter sp016795465	79.8152	785	1854	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482965.1	s__Prosthecobacter sp002482965	79.7843	877	1854	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903838675.1	s__Prosthecobacter sp903838675	79.7203	806	1854	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	99.92	99.91	0.96	0.96	3	-
GCA_002336895.1	s__Prosthecobacter sp002336895	79.5603	815	1854	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203095.1	s__Prosthecobacter vanneervenii	79.2549	813	1854	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:30:24,352] [INFO] GTDB search result was written to OceanDNA-b47088/result_gtdb.tsv
[2023-03-16 17:30:24,352] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:30:24,355] [INFO] DFAST_QC result json was written to OceanDNA-b47088/dqc_result.json
[2023-03-16 17:30:24,355] [INFO] DFAST_QC completed!
[2023-03-16 17:30:24,355] [INFO] Total running time: 0h5m15s