[2023-03-16 07:28:30,026] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:30,026] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:30,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d6eaadf-e3c5-4490-bb25-6f5de232c704/dqc_reference
[2023-03-16 07:28:31,182] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,182] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,182] [INFO] Running command: cat /var/lib/cwl/stg5b5b4d70-8693-4aff-8bc9-648c223a2b39/OceanDNA-b30373.fa | prodigal -d OceanDNA-b30373/cds.fna -a OceanDNA-b30373/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:54,351] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:54,351] [INFO] Task started: HMMsearch
[2023-03-16 07:28:54,351] [INFO] Running command: hmmsearch --tblout OceanDNA-b30373/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d6eaadf-e3c5-4490-bb25-6f5de232c704/dqc_reference/reference_markers.hmm OceanDNA-b30373/protein.faa > /dev/null
[2023-03-16 07:28:54,557] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:54,558] [INFO] Found 6/6 markers.
[2023-03-16 07:28:54,583] [INFO] Query marker FASTA was written to OceanDNA-b30373/markers.fasta
[2023-03-16 07:28:54,584] [INFO] Task started: Blastn
[2023-03-16 07:28:54,584] [INFO] Running command: blastn -query OceanDNA-b30373/markers.fasta -db /var/lib/cwl/stg1d6eaadf-e3c5-4490-bb25-6f5de232c704/dqc_reference/reference_markers.fasta -out OceanDNA-b30373/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:55,421] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:55,423] [INFO] Selected 20 target genomes.
[2023-03-16 07:28:55,423] [INFO] Target genome list was writen to OceanDNA-b30373/target_genomes.txt
[2023-03-16 07:28:55,436] [INFO] Task started: fastANI
[2023-03-16 07:28:55,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b5b4d70-8693-4aff-8bc9-648c223a2b39/OceanDNA-b30373.fa --refList OceanDNA-b30373/target_genomes.txt --output OceanDNA-b30373/fastani_result.tsv --threads 1
[2023-03-16 07:29:10,471] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:10,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d6eaadf-e3c5-4490-bb25-6f5de232c704/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:29:10,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d6eaadf-e3c5-4490-bb25-6f5de232c704/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:29:10,483] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:29:10,484] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:29:10,484] [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
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	80.9423	615	1202	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	80.6852	600	1202	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	80.187	529	1202	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.3021	429	1202	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.2886	432	1202	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.1592	464	1202	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	77.8967	357	1202	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.8855	370	1202	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.815	399	1202	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.8081	401	1202	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.7622	334	1202	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	77.7446	372	1202	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.7333	370	1202	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	77.1625	249	1202	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.9657	166	1202	95	below_threshold
Sulfitobacter guttiformis	strain=DSM 11458	GCA_003610455.1	74349	74349	type	True	76.9615	228	1202	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.9489	250	1202	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.6368	207	1202	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.4688	189	1202	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.4468	183	1202	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:29:10,484] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30373/tc_result.tsv
[2023-03-16 07:29:10,484] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:29:10,484] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:29:10,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d6eaadf-e3c5-4490-bb25-6f5de232c704/dqc_reference/checkm_data
[2023-03-16 07:29:10,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:29:10,548] [INFO] Task started: CheckM
[2023-03-16 07:29:10,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30373/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30373/checkm_input OceanDNA-b30373/checkm_result
[2023-03-16 07:30:08,651] [INFO] Task succeeded: CheckM
[2023-03-16 07:30:08,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:30:08,654] [INFO] ===== Completeness check finished =====
[2023-03-16 07:30:08,654] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:30:08,655] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30373/markers.fasta)
[2023-03-16 07:30:08,655] [INFO] Task started: Blastn
[2023-03-16 07:30:08,656] [INFO] Running command: blastn -query OceanDNA-b30373/markers.fasta -db /var/lib/cwl/stg1d6eaadf-e3c5-4490-bb25-6f5de232c704/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30373/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:30:09,984] [INFO] Task succeeded: Blastn
[2023-03-16 07:30:09,985] [INFO] Selected 11 target genomes.
[2023-03-16 07:30:09,985] [INFO] Target genome list was writen to OceanDNA-b30373/target_genomes_gtdb.txt
[2023-03-16 07:30:10,256] [INFO] Task started: fastANI
[2023-03-16 07:30:10,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b5b4d70-8693-4aff-8bc9-648c223a2b39/OceanDNA-b30373.fa --refList OceanDNA-b30373/target_genomes_gtdb.txt --output OceanDNA-b30373/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:30:19,519] [INFO] Task succeeded: fastANI
[2023-03-16 07:30:19,526] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:30:19,526] [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
GCF_000156335.1	s__Sulfitobacter sp000156335	97.4427	1157	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013282155.1	s__Sulfitobacter sp013282155	83.2314	729	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCA_013139555.1	s__Sulfitobacter sp013139555	81.3525	559	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	80.9698	612	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	80.7055	598	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_900103185.1	s__Sulfitobacter litoralis	80.1973	528	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_006064855.1	s__Sulfitobacter sp006064855	80.1007	535	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	78.2682	430	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611275.1	s__Sulfitobacter sp001634775	78.0632	390	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCA_003217735.2	s__Marinibacterium sp003217735	76.8132	321	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_009789075.1	s__Pseudooceanicola pacificus	76.6146	199	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:30:19,527] [INFO] GTDB search result was written to OceanDNA-b30373/result_gtdb.tsv
[2023-03-16 07:30:19,527] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:30:19,528] [INFO] DFAST_QC result json was written to OceanDNA-b30373/dqc_result.json
[2023-03-16 07:30:19,528] [INFO] DFAST_QC completed!
[2023-03-16 07:30:19,528] [INFO] Total running time: 0h1m50s