[2023-03-19 00:15:41,728] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,728] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg19b29881-6a7b-449d-857b-5813a14d9bf8/dqc_reference
[2023-03-19 00:15:43,441] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,441] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,441] [INFO] Running command: cat /var/lib/cwl/stgc7ebe64e-8376-4d67-a5fc-c111c9fa6872/OceanDNA-b30572.fa | prodigal -d OceanDNA-b30572/cds.fna -a OceanDNA-b30572/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:16:10,016] [INFO] Task succeeded: Prodigal
[2023-03-19 00:16:10,016] [INFO] Task started: HMMsearch
[2023-03-19 00:16:10,016] [INFO] Running command: hmmsearch --tblout OceanDNA-b30572/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19b29881-6a7b-449d-857b-5813a14d9bf8/dqc_reference/reference_markers.hmm OceanDNA-b30572/protein.faa > /dev/null
[2023-03-19 00:16:10,273] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:16:10,273] [INFO] Found 6/6 markers.
[2023-03-19 00:16:10,308] [INFO] Query marker FASTA was written to OceanDNA-b30572/markers.fasta
[2023-03-19 00:16:10,311] [INFO] Task started: Blastn
[2023-03-19 00:16:10,311] [INFO] Running command: blastn -query OceanDNA-b30572/markers.fasta -db /var/lib/cwl/stg19b29881-6a7b-449d-857b-5813a14d9bf8/dqc_reference/reference_markers.fasta -out OceanDNA-b30572/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:11,077] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:11,078] [INFO] Selected 21 target genomes.
[2023-03-19 00:16:11,079] [INFO] Target genome list was writen to OceanDNA-b30572/target_genomes.txt
[2023-03-19 00:16:11,095] [INFO] Task started: fastANI
[2023-03-19 00:16:11,095] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7ebe64e-8376-4d67-a5fc-c111c9fa6872/OceanDNA-b30572.fa --refList OceanDNA-b30572/target_genomes.txt --output OceanDNA-b30572/fastani_result.tsv --threads 1
[2023-03-19 00:16:27,775] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:27,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19b29881-6a7b-449d-857b-5813a14d9bf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:27,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19b29881-6a7b-449d-857b-5813a14d9bf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:27,789] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:27,789] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:16:27,789] [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
Tritonibacter scottomollicae	strain=DSM 25328	GCA_003003215.1	483013	483013	type	True	80.8986	791	1387	95	below_threshold
Tritonibacter mobilis	strain=DSM 23403	GCA_900106635.1	379347	379347	type	True	79.9525	691	1387	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	79.9499	693	1387	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	79.0277	566	1387	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	78.8891	525	1387	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.8628	575	1387	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.8403	543	1387	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	78.6266	479	1387	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.6191	521	1387	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	78.6151	487	1387	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	78.5533	448	1387	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	78.52	451	1387	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	78.4677	478	1387	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	78.4526	457	1387	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.3915	483	1387	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	78.3731	454	1387	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	78.0108	459	1387	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.2463	270	1387	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.2054	235	1387	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.0266	258	1387	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.0204	242	1387	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:16:27,790] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30572/tc_result.tsv
[2023-03-19 00:16:27,790] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:27,790] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:27,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19b29881-6a7b-449d-857b-5813a14d9bf8/dqc_reference/checkm_data
[2023-03-19 00:16:27,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:27,797] [INFO] Task started: CheckM
[2023-03-19 00:16:27,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30572/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30572/checkm_input OceanDNA-b30572/checkm_result
[2023-03-19 00:17:36,623] [INFO] Task succeeded: CheckM
[2023-03-19 00:17:36,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:17:36,627] [INFO] ===== Completeness check finished =====
[2023-03-19 00:17:36,627] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:17:36,627] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30572/markers.fasta)
[2023-03-19 00:17:36,628] [INFO] Task started: Blastn
[2023-03-19 00:17:36,628] [INFO] Running command: blastn -query OceanDNA-b30572/markers.fasta -db /var/lib/cwl/stg19b29881-6a7b-449d-857b-5813a14d9bf8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30572/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:17:37,881] [INFO] Task succeeded: Blastn
[2023-03-19 00:17:37,882] [INFO] Selected 13 target genomes.
[2023-03-19 00:17:37,883] [INFO] Target genome list was writen to OceanDNA-b30572/target_genomes_gtdb.txt
[2023-03-19 00:17:37,925] [INFO] Task started: fastANI
[2023-03-19 00:17:37,925] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7ebe64e-8376-4d67-a5fc-c111c9fa6872/OceanDNA-b30572.fa --refList OceanDNA-b30572/target_genomes_gtdb.txt --output OceanDNA-b30572/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:17:49,456] [INFO] Task succeeded: fastANI
[2023-03-19 00:17:49,464] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:17:49,464] [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_001874255.1	s__Epibacterium sp001874255	99.9781	1298	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006265095.1	s__Epibacterium sp006265095	88.3813	1102	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001518015.1	s__Epibacterium horizontis	81.5434	813	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806385.1	s__Epibacterium sp011806385	80.9311	692	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003215.1	s__Epibacterium scottomollicae	80.8824	793	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001681715.1	s__Epibacterium mobile	79.9287	695	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	97.01	96.41	0.91	0.87	56	-
GCF_000014065.1	s__Epibacterium sp000014065	79.717	660	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473145.1	s__Leisingera daeponensis	79.0201	566	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_013317235.1	s__Leisingera sp013317235	78.9142	528	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	78.836	543	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	78.634	512	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458415.1	s__Epibacterium multivorans	78.6182	480	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_013373325.1	s__Leisingera sp013373325	78.164	444	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:17:49,464] [INFO] GTDB search result was written to OceanDNA-b30572/result_gtdb.tsv
[2023-03-19 00:17:49,464] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:17:49,466] [INFO] DFAST_QC result json was written to OceanDNA-b30572/dqc_result.json
[2023-03-19 00:17:49,466] [INFO] DFAST_QC completed!
[2023-03-19 00:17:49,466] [INFO] Total running time: 0h2m8s