[2023-03-18 08:17:20,594] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:20,594] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:20,595] [INFO] DQC Reference Directory: /var/lib/cwl/stgca2d7f1b-4086-4dc1-b089-782eeada2e6c/dqc_reference
[2023-03-18 08:17:21,897] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:21,897] [INFO] Task started: Prodigal
[2023-03-18 08:17:21,897] [INFO] Running command: cat /var/lib/cwl/stg9e08a1d8-28c5-45ba-914b-8e3228f0284a/OceanDNA-b28045.fa | prodigal -d OceanDNA-b28045/cds.fna -a OceanDNA-b28045/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:36,134] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:36,135] [INFO] Task started: HMMsearch
[2023-03-18 08:17:36,135] [INFO] Running command: hmmsearch --tblout OceanDNA-b28045/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca2d7f1b-4086-4dc1-b089-782eeada2e6c/dqc_reference/reference_markers.hmm OceanDNA-b28045/protein.faa > /dev/null
[2023-03-18 08:17:36,358] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:36,358] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9e08a1d8-28c5-45ba-914b-8e3228f0284a/OceanDNA-b28045.fa]
[2023-03-18 08:17:36,378] [INFO] Query marker FASTA was written to OceanDNA-b28045/markers.fasta
[2023-03-18 08:17:36,378] [INFO] Task started: Blastn
[2023-03-18 08:17:36,379] [INFO] Running command: blastn -query OceanDNA-b28045/markers.fasta -db /var/lib/cwl/stgca2d7f1b-4086-4dc1-b089-782eeada2e6c/dqc_reference/reference_markers.fasta -out OceanDNA-b28045/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:36,990] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:36,991] [INFO] Selected 18 target genomes.
[2023-03-18 08:17:36,991] [INFO] Target genome list was writen to OceanDNA-b28045/target_genomes.txt
[2023-03-18 08:17:36,999] [INFO] Task started: fastANI
[2023-03-18 08:17:36,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e08a1d8-28c5-45ba-914b-8e3228f0284a/OceanDNA-b28045.fa --refList OceanDNA-b28045/target_genomes.txt --output OceanDNA-b28045/fastani_result.tsv --threads 1
[2023-03-18 08:17:48,601] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:48,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca2d7f1b-4086-4dc1-b089-782eeada2e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:48,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca2d7f1b-4086-4dc1-b089-782eeada2e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:48,609] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:48,609] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:17:48,610] [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
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	76.9297	189	736	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	76.5892	80	736	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	76.4021	119	736	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	76.3938	121	736	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.3361	102	736	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.2105	124	736	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.1983	125	736	95	below_threshold
Roseobacter litoralis	strain=Och 149	GCA_000154785.2	42443	42443	type	True	76.1695	54	736	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	75.8814	68	736	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	75.8738	51	736	95	below_threshold
Litorivita pollutaquae	strain=FSX-11	GCA_003205515.1	2200892	2200892	type	True	75.7425	54	736	95	below_threshold
Shimia gijangensis	strain=DSM 100564	GCA_900142085.1	1470563	1470563	type	True	75.7149	67	736	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:17:48,610] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28045/tc_result.tsv
[2023-03-18 08:17:48,610] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:48,610] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:48,610] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca2d7f1b-4086-4dc1-b089-782eeada2e6c/dqc_reference/checkm_data
[2023-03-18 08:17:48,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:48,621] [INFO] Task started: CheckM
[2023-03-18 08:17:48,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28045/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28045/checkm_input OceanDNA-b28045/checkm_result
[2023-03-18 08:18:28,000] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:28,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:28,003] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:28,003] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:28,003] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28045/markers.fasta)
[2023-03-18 08:18:28,004] [INFO] Task started: Blastn
[2023-03-18 08:18:28,004] [INFO] Running command: blastn -query OceanDNA-b28045/markers.fasta -db /var/lib/cwl/stgca2d7f1b-4086-4dc1-b089-782eeada2e6c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28045/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:28,803] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:28,804] [INFO] Selected 17 target genomes.
[2023-03-18 08:18:28,804] [INFO] Target genome list was writen to OceanDNA-b28045/target_genomes_gtdb.txt
[2023-03-18 08:18:28,906] [INFO] Task started: fastANI
[2023-03-18 08:18:28,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e08a1d8-28c5-45ba-914b-8e3228f0284a/OceanDNA-b28045.fa --refList OceanDNA-b28045/target_genomes_gtdb.txt --output OceanDNA-b28045/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:39,378] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:39,387] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:18:39,387] [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_905182355.1	s__Ascidiaceihabitans sp905182355	83.7209	528	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647275.1	s__Ascidiaceihabitans sp018647275	79.1287	167	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182105.1	s__Ascidiaceihabitans sp905182105	78.9122	287	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478745.1	s__Ascidiaceihabitans sp002478745	78.8926	302	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.75	99.75	0.89	0.89	2	-
GCF_900302465.1	s__Ascidiaceihabitans donghaensis	76.9178	190	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103185.1	s__Sulfitobacter litoralis	76.5892	80	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_013282155.1	s__Sulfitobacter sp013282155	76.5736	114	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	76.471	132	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.3361	116	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_900116285.1	s__Sulfitobacter marinus	76.3361	102	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	76.3147	116	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006064855.1	s__Sulfitobacter sp006064855	76.0218	95	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854675.1	s__Sulfitobacter sp017854675	75.9232	110	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205515.1	s__Litorivita pollutaquae	75.7425	54	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorivita	95.0	98.23	98.23	0.93	0.93	2	-
GCF_003201935.1	s__Yoonia sp003201935	75.7175	54	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:39,387] [INFO] GTDB search result was written to OceanDNA-b28045/result_gtdb.tsv
[2023-03-18 08:18:39,387] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:39,389] [INFO] DFAST_QC result json was written to OceanDNA-b28045/dqc_result.json
[2023-03-18 08:18:39,389] [INFO] DFAST_QC completed!
[2023-03-18 08:18:39,389] [INFO] Total running time: 0h1m19s