[2023-03-19 00:44:19,945] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:44:19,946] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:44:19,946] [INFO] DQC Reference Directory: /var/lib/cwl/stga1343ae1-9f0a-4948-a79f-3b7bf6b790c4/dqc_reference
[2023-03-19 00:44:21,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:44:21,046] [INFO] Task started: Prodigal
[2023-03-19 00:44:21,046] [INFO] Running command: cat /var/lib/cwl/stgb36b1575-ea17-4b3b-87bd-c9208f473f51/OceanDNA-b41474.fa | prodigal -d OceanDNA-b41474/cds.fna -a OceanDNA-b41474/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:44:42,917] [INFO] Task succeeded: Prodigal
[2023-03-19 00:44:42,917] [INFO] Task started: HMMsearch
[2023-03-19 00:44:42,917] [INFO] Running command: hmmsearch --tblout OceanDNA-b41474/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1343ae1-9f0a-4948-a79f-3b7bf6b790c4/dqc_reference/reference_markers.hmm OceanDNA-b41474/protein.faa > /dev/null
[2023-03-19 00:44:43,140] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:44:43,140] [INFO] Found 6/6 markers.
[2023-03-19 00:44:43,162] [INFO] Query marker FASTA was written to OceanDNA-b41474/markers.fasta
[2023-03-19 00:44:43,162] [INFO] Task started: Blastn
[2023-03-19 00:44:43,162] [INFO] Running command: blastn -query OceanDNA-b41474/markers.fasta -db /var/lib/cwl/stga1343ae1-9f0a-4948-a79f-3b7bf6b790c4/dqc_reference/reference_markers.fasta -out OceanDNA-b41474/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:44:43,856] [INFO] Task succeeded: Blastn
[2023-03-19 00:44:43,857] [INFO] Selected 20 target genomes.
[2023-03-19 00:44:43,857] [INFO] Target genome list was writen to OceanDNA-b41474/target_genomes.txt
[2023-03-19 00:44:43,869] [INFO] Task started: fastANI
[2023-03-19 00:44:43,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgb36b1575-ea17-4b3b-87bd-c9208f473f51/OceanDNA-b41474.fa --refList OceanDNA-b41474/target_genomes.txt --output OceanDNA-b41474/fastani_result.tsv --threads 1
[2023-03-19 00:44:57,604] [INFO] Task succeeded: fastANI
[2023-03-19 00:44:57,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1343ae1-9f0a-4948-a79f-3b7bf6b790c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:44:57,604] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1343ae1-9f0a-4948-a79f-3b7bf6b790c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:44:57,613] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 00:44:57,613] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 00:44:57,614] [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
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	98.0056	1089	1179	95	conclusive
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	78.4237	282	1179	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	78.0378	220	1179	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	77.9355	227	1179	95	below_threshold
Zhongshania antarctica	strain=DSM 25701	GCA_014202945.1	641702	641702	type	True	77.658	169	1179	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	77.6519	171	1179	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	77.6067	192	1179	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	77.1409	60	1179	95	below_threshold
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	76.3607	55	1179	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	76.1864	59	1179	95	below_threshold
Pseudomonas taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	75.9845	65	1179	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	75.9227	54	1179	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	75.9125	53	1179	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	75.8066	60	1179	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:44:57,614] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41474/tc_result.tsv
[2023-03-19 00:44:57,614] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:44:57,614] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:44:57,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1343ae1-9f0a-4948-a79f-3b7bf6b790c4/dqc_reference/checkm_data
[2023-03-19 00:44:57,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:44:57,643] [INFO] Task started: CheckM
[2023-03-19 00:44:57,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41474/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41474/checkm_input OceanDNA-b41474/checkm_result
[2023-03-19 00:45:52,016] [INFO] Task succeeded: CheckM
[2023-03-19 00:45:52,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:45:52,019] [INFO] ===== Completeness check finished =====
[2023-03-19 00:45:52,019] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:45:52,020] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41474/markers.fasta)
[2023-03-19 00:45:52,021] [INFO] Task started: Blastn
[2023-03-19 00:45:52,021] [INFO] Running command: blastn -query OceanDNA-b41474/markers.fasta -db /var/lib/cwl/stga1343ae1-9f0a-4948-a79f-3b7bf6b790c4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41474/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:45:53,178] [INFO] Task succeeded: Blastn
[2023-03-19 00:45:53,179] [INFO] Selected 17 target genomes.
[2023-03-19 00:45:53,179] [INFO] Target genome list was writen to OceanDNA-b41474/target_genomes_gtdb.txt
[2023-03-19 00:45:53,196] [INFO] Task started: fastANI
[2023-03-19 00:45:53,196] [INFO] Running command: fastANI --query /var/lib/cwl/stgb36b1575-ea17-4b3b-87bd-c9208f473f51/OceanDNA-b41474.fa --refList OceanDNA-b41474/target_genomes_gtdb.txt --output OceanDNA-b41474/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:46:04,510] [INFO] Task succeeded: fastANI
[2023-03-19 00:46:04,519] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:46:04,519] [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_012272835.1	s__Spongiibacter sp012272835	98.0223	1088	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016906995.1	s__Spongiibacter marinus	78.7097	248	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	97.69	97.65	0.87	0.86	3	-
GCF_000422345.1	s__Spongiibacter marinus_A	78.5077	240	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420325.1	s__Spongiibacter tropicus	78.4292	281	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	98.00	97.89	0.92	0.88	9	-
GCF_016132545.1	s__CSC3-9 sp016132545	77.9346	227	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__CSC3-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705705.1	s__KMU-158 sp014705705	77.6071	192	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__KMU-158	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010805.1	s__IMCC21906 sp001010805	77.5483	171	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__IMCC21906	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705855.1	s__Marortus aliphaticivorans_B	77.5286	152	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191715.1	s__Litorivivens lipolytica	76.9584	163	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066965.1	s__Marortus sp018066965	76.7286	131	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.2822	88	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829415.1	s__Pseudomonas_E sp000829415	76.0528	51	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498575.2	s__Pseudomonas_E taeanensis	75.9845	65	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309075.1	s__Motiliproteus sp017309075	75.8685	57	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:46:04,519] [INFO] GTDB search result was written to OceanDNA-b41474/result_gtdb.tsv
[2023-03-19 00:46:04,519] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:46:04,521] [INFO] DFAST_QC result json was written to OceanDNA-b41474/dqc_result.json
[2023-03-19 00:46:04,521] [INFO] DFAST_QC completed!
[2023-03-19 00:46:04,521] [INFO] Total running time: 0h1m45s