[2023-03-16 04:24:46,333] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:24:46,333] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:24:46,333] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd75395d-aa99-459e-bc37-7a039eaf478c/dqc_reference
[2023-03-16 04:24:48,114] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:24:48,114] [INFO] Task started: Prodigal
[2023-03-16 04:24:48,114] [INFO] Running command: cat /var/lib/cwl/stg5dc0a628-b9e0-41fc-aee9-896ffae54c92/OceanDNA-b28050.fa | prodigal -d OceanDNA-b28050/cds.fna -a OceanDNA-b28050/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:25:02,136] [INFO] Task succeeded: Prodigal
[2023-03-16 04:25:02,137] [INFO] Task started: HMMsearch
[2023-03-16 04:25:02,137] [INFO] Running command: hmmsearch --tblout OceanDNA-b28050/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd75395d-aa99-459e-bc37-7a039eaf478c/dqc_reference/reference_markers.hmm OceanDNA-b28050/protein.faa > /dev/null
[2023-03-16 04:25:02,372] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:25:02,372] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5dc0a628-b9e0-41fc-aee9-896ffae54c92/OceanDNA-b28050.fa]
[2023-03-16 04:25:02,392] [INFO] Query marker FASTA was written to OceanDNA-b28050/markers.fasta
[2023-03-16 04:25:02,393] [INFO] Task started: Blastn
[2023-03-16 04:25:02,393] [INFO] Running command: blastn -query OceanDNA-b28050/markers.fasta -db /var/lib/cwl/stgdd75395d-aa99-459e-bc37-7a039eaf478c/dqc_reference/reference_markers.fasta -out OceanDNA-b28050/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:02,965] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:02,966] [INFO] Selected 21 target genomes.
[2023-03-16 04:25:02,966] [INFO] Target genome list was writen to OceanDNA-b28050/target_genomes.txt
[2023-03-16 04:25:02,979] [INFO] Task started: fastANI
[2023-03-16 04:25:02,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dc0a628-b9e0-41fc-aee9-896ffae54c92/OceanDNA-b28050.fa --refList OceanDNA-b28050/target_genomes.txt --output OceanDNA-b28050/fastani_result.tsv --threads 1
[2023-03-16 04:25:16,688] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:16,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd75395d-aa99-459e-bc37-7a039eaf478c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:25:16,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd75395d-aa99-459e-bc37-7a039eaf478c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:25:16,698] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:25:16,698] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:25:16,698] [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	76.7237	173	710	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	76.3799	81	710	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	76.349	81	710	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.3428	101	710	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	76.0916	74	710	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.0611	88	710	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.0611	88	710	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	75.9062	102	710	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	75.8859	102	710	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	75.8712	52	710	95	below_threshold
Roseobacter ponti	strain=DSM 106830	GCA_012932215.1	1891787	1891787	type	True	75.8157	57	710	95	below_threshold
Roseobacter denitrificans	strain=OCh 114	GCA_000014045.1	2434	2434	type	True	75.6814	59	710	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	75.6285	63	710	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:25:16,698] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28050/tc_result.tsv
[2023-03-16 04:25:16,698] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:25:16,698] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:25:16,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd75395d-aa99-459e-bc37-7a039eaf478c/dqc_reference/checkm_data
[2023-03-16 04:25:16,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:25:16,703] [INFO] Task started: CheckM
[2023-03-16 04:25:16,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28050/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28050/checkm_input OceanDNA-b28050/checkm_result
[2023-03-16 04:25:55,401] [INFO] Task succeeded: CheckM
[2023-03-16 04:25:55,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.09%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:25:55,404] [INFO] ===== Completeness check finished =====
[2023-03-16 04:25:55,404] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:25:55,405] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28050/markers.fasta)
[2023-03-16 04:25:55,406] [INFO] Task started: Blastn
[2023-03-16 04:25:55,406] [INFO] Running command: blastn -query OceanDNA-b28050/markers.fasta -db /var/lib/cwl/stgdd75395d-aa99-459e-bc37-7a039eaf478c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28050/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:56,265] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:56,266] [INFO] Selected 17 target genomes.
[2023-03-16 04:25:56,266] [INFO] Target genome list was writen to OceanDNA-b28050/target_genomes_gtdb.txt
[2023-03-16 04:25:56,287] [INFO] Task started: fastANI
[2023-03-16 04:25:56,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dc0a628-b9e0-41fc-aee9-896ffae54c92/OceanDNA-b28050.fa --refList OceanDNA-b28050/target_genomes_gtdb.txt --output OceanDNA-b28050/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:26:06,994] [INFO] Task succeeded: fastANI
[2023-03-16 04:26:07,003] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:26:07,004] [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	98.7444	608	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002478745.1	s__Ascidiaceihabitans sp002478745	78.2021	301	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.75	99.75	0.89	0.89	2	-
GCA_905182105.1	s__Ascidiaceihabitans sp905182105	78.0638	279	710	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	77.9021	170	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302465.1	s__Ascidiaceihabitans donghaensis	76.7237	173	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	76.3604	105	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.3339	108	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_003352065.1	s__Sulfitobacter sp003352065	76.2428	93	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	76.1801	93	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCA_017854855.1	s__Sulfitobacter sp017854855	76.1616	90	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.0611	88	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	75.9443	94	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	75.8913	98	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002087335.1	s__Pseudophaeobacter leonis	75.8542	51	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	75.7633	60	710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:26:07,004] [INFO] GTDB search result was written to OceanDNA-b28050/result_gtdb.tsv
[2023-03-16 04:26:07,004] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:26:07,006] [INFO] DFAST_QC result json was written to OceanDNA-b28050/dqc_result.json
[2023-03-16 04:26:07,006] [INFO] DFAST_QC completed!
[2023-03-16 04:26:07,006] [INFO] Total running time: 0h1m21s