[2023-03-19 04:11:06,929] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,929] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg776075ad-1446-430f-b591-cd85ee9fa3f6/dqc_reference
[2023-03-19 04:11:08,644] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,645] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,645] [INFO] Running command: cat /var/lib/cwl/stga0fb965c-b94f-466d-b72d-062a684d15fd/OceanDNA-b30155.fa | prodigal -d OceanDNA-b30155/cds.fna -a OceanDNA-b30155/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:20,548] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:20,549] [INFO] Task started: HMMsearch
[2023-03-19 04:11:20,549] [INFO] Running command: hmmsearch --tblout OceanDNA-b30155/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg776075ad-1446-430f-b591-cd85ee9fa3f6/dqc_reference/reference_markers.hmm OceanDNA-b30155/protein.faa > /dev/null
[2023-03-19 04:11:20,700] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:20,700] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga0fb965c-b94f-466d-b72d-062a684d15fd/OceanDNA-b30155.fa]
[2023-03-19 04:11:20,719] [INFO] Query marker FASTA was written to OceanDNA-b30155/markers.fasta
[2023-03-19 04:11:20,720] [INFO] Task started: Blastn
[2023-03-19 04:11:20,720] [INFO] Running command: blastn -query OceanDNA-b30155/markers.fasta -db /var/lib/cwl/stg776075ad-1446-430f-b591-cd85ee9fa3f6/dqc_reference/reference_markers.fasta -out OceanDNA-b30155/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:21,281] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:21,282] [INFO] Selected 20 target genomes.
[2023-03-19 04:11:21,282] [INFO] Target genome list was writen to OceanDNA-b30155/target_genomes.txt
[2023-03-19 04:11:21,295] [INFO] Task started: fastANI
[2023-03-19 04:11:21,295] [INFO] Running command: fastANI --query /var/lib/cwl/stga0fb965c-b94f-466d-b72d-062a684d15fd/OceanDNA-b30155.fa --refList OceanDNA-b30155/target_genomes.txt --output OceanDNA-b30155/fastani_result.tsv --threads 1
[2023-03-19 04:11:33,767] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:33,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg776075ad-1446-430f-b591-cd85ee9fa3f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:33,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg776075ad-1446-430f-b591-cd85ee9fa3f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:33,776] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:33,776] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:11:33,776] [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
Boseongicola aestuarii	strain=CECT 8489	GCA_900184815.1	1470561	1470561	type	True	76.7367	70	583	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.7073	59	583	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.7065	59	583	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	76.4579	80	583	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	76.3912	94	583	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	76.3806	63	583	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	76.2784	56	583	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	76.2697	68	583	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	76.1661	53	583	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.1346	51	583	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	76.0143	65	583	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	75.9018	59	583	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.882	54	583	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:11:33,776] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30155/tc_result.tsv
[2023-03-19 04:11:33,777] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:33,777] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:33,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg776075ad-1446-430f-b591-cd85ee9fa3f6/dqc_reference/checkm_data
[2023-03-19 04:11:33,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:33,784] [INFO] Task started: CheckM
[2023-03-19 04:11:33,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30155/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30155/checkm_input OceanDNA-b30155/checkm_result
[2023-03-19 04:12:07,504] [INFO] Task succeeded: CheckM
[2023-03-19 04:12:07,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:12:07,506] [INFO] ===== Completeness check finished =====
[2023-03-19 04:12:07,506] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:12:07,506] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30155/markers.fasta)
[2023-03-19 04:12:07,507] [INFO] Task started: Blastn
[2023-03-19 04:12:07,507] [INFO] Running command: blastn -query OceanDNA-b30155/markers.fasta -db /var/lib/cwl/stg776075ad-1446-430f-b591-cd85ee9fa3f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30155/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:12:08,238] [INFO] Task succeeded: Blastn
[2023-03-19 04:12:08,239] [INFO] Selected 20 target genomes.
[2023-03-19 04:12:08,239] [INFO] Target genome list was writen to OceanDNA-b30155/target_genomes_gtdb.txt
[2023-03-19 04:12:08,325] [INFO] Task started: fastANI
[2023-03-19 04:12:08,326] [INFO] Running command: fastANI --query /var/lib/cwl/stga0fb965c-b94f-466d-b72d-062a684d15fd/OceanDNA-b30155.fa --refList OceanDNA-b30155/target_genomes_gtdb.txt --output OceanDNA-b30155/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:12:20,592] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:20,601] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:12:20,601] [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_013002465.1	s__JABDJO01 sp013002465	77.1949	159	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114635.1	s__Shimia aestuarii	76.9185	53	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	76.8246	88	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002079305.1	s__Rhodovulum sp002079305	76.4184	63	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944755.1	s__Rhodovulum robiginosum	76.2697	68	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116005.1	s__Poseidonocella sedimentorum	76.2336	58	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	76.1734	64	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142295.1	s__Vannielia litorea	76.1729	64	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526275.1	s__Lutimaribacter sp000526275	76.1096	82	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188335.1	s__Tropicimonas sediminicola	76.0893	77	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	76.0318	52	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	76.0223	100	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152725.1	s__Pseudooceanicola batsensis	75.9666	69	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142935.1	s__Rhodovulum sp900142935	75.9662	74	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018798885.1	s__Gemmobacter sp018798885	75.882	54	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-19 04:12:20,601] [INFO] GTDB search result was written to OceanDNA-b30155/result_gtdb.tsv
[2023-03-19 04:12:20,601] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:12:20,603] [INFO] DFAST_QC result json was written to OceanDNA-b30155/dqc_result.json
[2023-03-19 04:12:20,603] [INFO] DFAST_QC completed!
[2023-03-19 04:12:20,603] [INFO] Total running time: 0h1m14s