[2023-03-15 05:16:58,316] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:16:58,317] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:16:58,317] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c47137c-f77d-4e72-a7d8-7ad25fd37010/dqc_reference
[2023-03-15 05:16:59,412] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:16:59,413] [INFO] Task started: Prodigal
[2023-03-15 05:16:59,413] [INFO] Running command: cat /var/lib/cwl/stg04d37124-d6fd-4724-a58d-e70370145946/OceanDNA-b33521.fa | prodigal -d OceanDNA-b33521/cds.fna -a OceanDNA-b33521/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:17:10,870] [INFO] Task succeeded: Prodigal
[2023-03-15 05:17:10,870] [INFO] Task started: HMMsearch
[2023-03-15 05:17:10,870] [INFO] Running command: hmmsearch --tblout OceanDNA-b33521/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c47137c-f77d-4e72-a7d8-7ad25fd37010/dqc_reference/reference_markers.hmm OceanDNA-b33521/protein.faa > /dev/null
[2023-03-15 05:17:11,042] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:17:11,043] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg04d37124-d6fd-4724-a58d-e70370145946/OceanDNA-b33521.fa]
[2023-03-15 05:17:11,074] [INFO] Query marker FASTA was written to OceanDNA-b33521/markers.fasta
[2023-03-15 05:17:11,075] [INFO] Task started: Blastn
[2023-03-15 05:17:11,075] [INFO] Running command: blastn -query OceanDNA-b33521/markers.fasta -db /var/lib/cwl/stg8c47137c-f77d-4e72-a7d8-7ad25fd37010/dqc_reference/reference_markers.fasta -out OceanDNA-b33521/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:17:11,621] [INFO] Task succeeded: Blastn
[2023-03-15 05:17:11,623] [INFO] Selected 15 target genomes.
[2023-03-15 05:17:11,624] [INFO] Target genome list was writen to OceanDNA-b33521/target_genomes.txt
[2023-03-15 05:17:11,634] [INFO] Task started: fastANI
[2023-03-15 05:17:11,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d37124-d6fd-4724-a58d-e70370145946/OceanDNA-b33521.fa --refList OceanDNA-b33521/target_genomes.txt --output OceanDNA-b33521/fastani_result.tsv --threads 1
[2023-03-15 05:17:23,035] [INFO] Task succeeded: fastANI
[2023-03-15 05:17:23,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c47137c-f77d-4e72-a7d8-7ad25fd37010/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:17:23,036] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c47137c-f77d-4e72-a7d8-7ad25fd37010/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:17:23,044] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:17:23,044] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:17:23,044] [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
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	79.2409	157	362	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.1317	123	362	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.0561	153	362	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	79.0179	136	362	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.8923	138	362	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	78.8877	127	362	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	78.8356	158	362	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.7253	152	362	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	78.6942	152	362	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	77.7182	123	362	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	77.7	126	362	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	77.2694	85	362	95	below_threshold
Duganella levis	strain=CY42W	GCA_009857605.1	2692169	2692169	type	True	75.8463	55	362	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:17:23,046] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33521/tc_result.tsv
[2023-03-15 05:17:23,047] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:17:23,047] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:17:23,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c47137c-f77d-4e72-a7d8-7ad25fd37010/dqc_reference/checkm_data
[2023-03-15 05:17:23,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:17:23,139] [INFO] Task started: CheckM
[2023-03-15 05:17:23,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33521/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33521/checkm_input OceanDNA-b33521/checkm_result
[2023-03-15 05:17:55,819] [INFO] Task succeeded: CheckM
[2023-03-15 05:17:55,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.51%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:17:55,872] [INFO] ===== Completeness check finished =====
[2023-03-15 05:17:55,872] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:17:55,872] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33521/markers.fasta)
[2023-03-15 05:17:55,873] [INFO] Task started: Blastn
[2023-03-15 05:17:55,873] [INFO] Running command: blastn -query OceanDNA-b33521/markers.fasta -db /var/lib/cwl/stg8c47137c-f77d-4e72-a7d8-7ad25fd37010/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33521/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:17:56,678] [INFO] Task succeeded: Blastn
[2023-03-15 05:17:56,692] [INFO] Selected 14 target genomes.
[2023-03-15 05:17:56,692] [INFO] Target genome list was writen to OceanDNA-b33521/target_genomes_gtdb.txt
[2023-03-15 05:17:56,710] [INFO] Task started: fastANI
[2023-03-15 05:17:56,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d37124-d6fd-4724-a58d-e70370145946/OceanDNA-b33521.fa --refList OceanDNA-b33521/target_genomes_gtdb.txt --output OceanDNA-b33521/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:18:06,404] [INFO] Task succeeded: fastANI
[2023-03-15 05:18:06,412] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:18:06,413] [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_018063505.1	s__CAISIP01 sp018063505	81.1308	207	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAISIP01	95.0	99.51	99.51	0.88	0.88	2	-
GCA_016790475.1	s__CAISIP01 sp016790475	80.577	171	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAISIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503335.1	s__SCMQ01 sp005503335	80.2178	161	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCA_001797315.1	s__Hylemonella sp001797315	79.4815	118	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.98	99.98	0.98	0.98	2	-
GCA_002842205.1	s__PHCI01 sp002842205	78.8687	116	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PHCI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879655.1	s__JAABQG01 sp014879655	78.8405	116	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013693755.1	s__Tibeticola sp013693755	78.7858	120	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	96.98	96.98	0.89	0.89	2	-
GCA_006227825.1	s__Hydrogenophaga sp006227825	78.6804	107	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382045.1	s__Variovorax paradoxus_A	78.6318	158	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.57	98.47	0.92	0.91	6	-
GCA_011391155.1	s__JAABQG01 sp011391155	78.5518	94	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837145.1	s__BK-30 sp002837145	78.4042	103	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__BK-30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897615.1	s__Ottowia sp001897615	78.2044	134	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	96.20	96.20	0.84	0.84	2	-
GCA_903960915.1	s__Rhodoferax sp903960915	77.1423	65	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.23	97.99	0.89	0.81	4	-
GCA_014879745.1	s__CAIKUF01 sp014879745	76.8756	92	362	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:18:06,417] [INFO] GTDB search result was written to OceanDNA-b33521/result_gtdb.tsv
[2023-03-15 05:18:06,430] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:18:06,435] [INFO] DFAST_QC result json was written to OceanDNA-b33521/dqc_result.json
[2023-03-15 05:18:06,435] [INFO] DFAST_QC completed!
[2023-03-15 05:18:06,435] [INFO] Total running time: 0h1m8s