[2023-03-15 03:14:16,407] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,407] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,407] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3336817-fabd-4d6c-bfe8-bb1eb370dda1/dqc_reference
[2023-03-15 03:14:17,578] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,578] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,578] [INFO] Running command: cat /var/lib/cwl/stgbe96d108-ae15-4595-8a24-26e86400412a/OceanDNA-b43414.fa | prodigal -d OceanDNA-b43414/cds.fna -a OceanDNA-b43414/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:27,190] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:27,190] [INFO] Task started: HMMsearch
[2023-03-15 03:14:27,190] [INFO] Running command: hmmsearch --tblout OceanDNA-b43414/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3336817-fabd-4d6c-bfe8-bb1eb370dda1/dqc_reference/reference_markers.hmm OceanDNA-b43414/protein.faa > /dev/null
[2023-03-15 03:14:27,399] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:27,399] [INFO] Found 6/6 markers.
[2023-03-15 03:14:27,412] [INFO] Query marker FASTA was written to OceanDNA-b43414/markers.fasta
[2023-03-15 03:14:27,412] [INFO] Task started: Blastn
[2023-03-15 03:14:27,412] [INFO] Running command: blastn -query OceanDNA-b43414/markers.fasta -db /var/lib/cwl/stgd3336817-fabd-4d6c-bfe8-bb1eb370dda1/dqc_reference/reference_markers.fasta -out OceanDNA-b43414/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:28,019] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:28,020] [INFO] Selected 24 target genomes.
[2023-03-15 03:14:28,020] [INFO] Target genome list was writen to OceanDNA-b43414/target_genomes.txt
[2023-03-15 03:14:28,055] [INFO] Task started: fastANI
[2023-03-15 03:14:28,055] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe96d108-ae15-4595-8a24-26e86400412a/OceanDNA-b43414.fa --refList OceanDNA-b43414/target_genomes.txt --output OceanDNA-b43414/fastani_result.tsv --threads 1
[2023-03-15 03:14:40,119] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:40,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3336817-fabd-4d6c-bfe8-bb1eb370dda1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:14:40,120] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3336817-fabd-4d6c-bfe8-bb1eb370dda1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:14:40,126] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:14:40,126] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:14:40,126] [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
Thiomicrorhabdus sediminis	strain=G1	GCA_005885815.1	2580412	2580412	type	True	77.8893	94	588	95	below_threshold
Thiomicrorhabdus immobilis	strain=Am19	GCA_021654855.1	2791037	2791037	type	True	77.8174	123	588	95	below_threshold
Thiomicrorhabdus indica	strain=13-15A	GCA_004293625.1	2267253	2267253	type	True	77.5306	93	588	95	below_threshold
Thiomicrorhabdus xiamenensis	strain=G2	GCA_013282625.1	2739063	2739063	type	True	77.4077	57	588	95	below_threshold
Hydrogenovibrio kuenenii	strain=DSM 12350	GCA_000526715.1	63658	63658	type	True	76.9517	61	588	95	below_threshold
Thiomicrorhabdus aquaedulcis	strain=HaS4	GCA_004001325.1	2211106	2211106	type	True	76.6156	61	588	95	below_threshold
Thiomicrorhabdus arctica	strain=DSM 13458	GCA_000381085.1	131540	131540	type	True	76.5485	76	588	95	below_threshold
Thiosulfativibrio zosterae	strain=AkT22	GCA_011398155.1	2675053	2675053	type	True	76.3309	60	588	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:14:40,127] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43414/tc_result.tsv
[2023-03-15 03:14:40,127] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:14:40,127] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:14:40,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3336817-fabd-4d6c-bfe8-bb1eb370dda1/dqc_reference/checkm_data
[2023-03-15 03:14:40,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:14:40,131] [INFO] Task started: CheckM
[2023-03-15 03:14:40,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43414/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43414/checkm_input OceanDNA-b43414/checkm_result
[2023-03-15 03:15:09,007] [INFO] Task succeeded: CheckM
[2023-03-15 03:15:09,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 03:15:09,010] [INFO] ===== Completeness check finished =====
[2023-03-15 03:15:09,010] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:15:09,010] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43414/markers.fasta)
[2023-03-15 03:15:09,010] [INFO] Task started: Blastn
[2023-03-15 03:15:09,010] [INFO] Running command: blastn -query OceanDNA-b43414/markers.fasta -db /var/lib/cwl/stgd3336817-fabd-4d6c-bfe8-bb1eb370dda1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43414/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:15:10,008] [INFO] Task succeeded: Blastn
[2023-03-15 03:15:10,009] [INFO] Selected 19 target genomes.
[2023-03-15 03:15:10,009] [INFO] Target genome list was writen to OceanDNA-b43414/target_genomes_gtdb.txt
[2023-03-15 03:15:10,029] [INFO] Task started: fastANI
[2023-03-15 03:15:10,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe96d108-ae15-4595-8a24-26e86400412a/OceanDNA-b43414.fa --refList OceanDNA-b43414/target_genomes_gtdb.txt --output OceanDNA-b43414/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:15:17,209] [INFO] Task succeeded: fastANI
[2023-03-15 03:15:17,217] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:15:17,217] [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_000478585.1	s__Thiomicrorhabdus sp000478585	78.021	156	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885815.1	s__Thiomicrorhabdus sediminis	77.8893	94	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299245.1	s__Thiomicrorhabdus sp002299245	77.8752	89	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	99.68	99.68	0.83	0.83	2	-
GCF_000702325.1	s__Thiomicrorhabdus sp000702325	77.578	145	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571465.1	s__Thiomicrorhabdus sp017571465	77.4866	74	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526715.1	s__Hydrogenovibrio kuenenii	76.9517	61	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013153955.1	s__Thiomicrorhabdus sp013153955	76.8966	55	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006222135.1	s__Thiomicrorhabdus sp006222135	76.8075	75	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487015.1	s__Thiomicrorhabdus sp015487015	76.7073	53	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487495.1	s__Thiomicrorhabdus sp015487495	76.6729	70	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001325.1	s__Thiomicrorhabdus aquaedulcis	76.6156	61	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938655.1	s__Thiomicrorhabdus sp016938655	76.5699	82	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381085.1	s__Thiomicrorhabdus arctica	76.5485	76	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011398155.1	s__Thiosulfativibrio zosterae	76.3309	60	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiosulfativibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:15:17,218] [INFO] GTDB search result was written to OceanDNA-b43414/result_gtdb.tsv
[2023-03-15 03:15:17,218] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:15:17,219] [INFO] DFAST_QC result json was written to OceanDNA-b43414/dqc_result.json
[2023-03-15 03:15:17,219] [INFO] DFAST_QC completed!
[2023-03-15 03:15:17,219] [INFO] Total running time: 0h1m1s