[2023-03-16 22:45:35,374] [INFO] DFAST_QC pipeline started.
[2023-03-16 22:45:35,374] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 22:45:35,374] [INFO] DQC Reference Directory: /var/lib/cwl/stgc22a480d-ecfb-4c12-8c16-a35f71a8e187/dqc_reference
[2023-03-16 22:45:37,282] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 22:45:37,282] [INFO] Task started: Prodigal
[2023-03-16 22:45:37,282] [INFO] Running command: cat /var/lib/cwl/stg86ad4d74-d0f4-4543-af2d-1fb55593fe47/OceanDNA-b17190.fa | prodigal -d OceanDNA-b17190/cds.fna -a OceanDNA-b17190/protein.faa -g 11 -q > /dev/null
[2023-03-16 22:45:45,237] [INFO] Task succeeded: Prodigal
[2023-03-16 22:45:45,238] [INFO] Task started: HMMsearch
[2023-03-16 22:45:45,238] [INFO] Running command: hmmsearch --tblout OceanDNA-b17190/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc22a480d-ecfb-4c12-8c16-a35f71a8e187/dqc_reference/reference_markers.hmm OceanDNA-b17190/protein.faa > /dev/null
[2023-03-16 22:45:45,424] [INFO] Task succeeded: HMMsearch
[2023-03-16 22:45:45,425] [INFO] Found 6/6 markers.
[2023-03-16 22:45:45,439] [INFO] Query marker FASTA was written to OceanDNA-b17190/markers.fasta
[2023-03-16 22:45:45,439] [INFO] Task started: Blastn
[2023-03-16 22:45:45,439] [INFO] Running command: blastn -query OceanDNA-b17190/markers.fasta -db /var/lib/cwl/stgc22a480d-ecfb-4c12-8c16-a35f71a8e187/dqc_reference/reference_markers.fasta -out OceanDNA-b17190/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:45:45,942] [INFO] Task succeeded: Blastn
[2023-03-16 22:45:45,943] [INFO] Selected 13 target genomes.
[2023-03-16 22:45:45,943] [INFO] Target genome list was writen to OceanDNA-b17190/target_genomes.txt
[2023-03-16 22:45:45,951] [INFO] Task started: fastANI
[2023-03-16 22:45:45,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg86ad4d74-d0f4-4543-af2d-1fb55593fe47/OceanDNA-b17190.fa --refList OceanDNA-b17190/target_genomes.txt --output OceanDNA-b17190/fastani_result.tsv --threads 1
[2023-03-16 22:45:52,158] [INFO] Task succeeded: fastANI
[2023-03-16 22:45:52,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc22a480d-ecfb-4c12-8c16-a35f71a8e187/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 22:45:52,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc22a480d-ecfb-4c12-8c16-a35f71a8e187/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 22:45:52,166] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 22:45:52,166] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 22:45:52,166] [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
Cetobacterium ceti	strain=ATCC 700028	GCA_900167275.1	180163	180163	type	True	97.0269	496	530	95	conclusive
Cetobacterium somerae	strain=ATCC BAA-474	GCA_000479045.1	188913	188913	type	True	77.7419	206	530	95	below_threshold
Fusobacterium ulcerans	strain=ATCC 49185	GCA_000158315.2	861	861	type	True	77.2011	131	530	95	below_threshold
Fusobacterium ulcerans	strain=ATCC 49185	GCA_003019675.1	861	861	type	True	77.1834	132	530	95	below_threshold
Fusobacterium necrogenes	strain=NCTC10723	GCA_900450765.1	858	858	type	True	77.1602	114	530	95	below_threshold
Fusobacterium perfoetens	strain=ATCC 29250	GCA_000622245.1	852	852	type	True	76.7103	139	530	95	below_threshold
Ilyobacter polytropus	strain=DSM 2926	GCA_000165505.1	167642	167642	type	True	76.4913	55	530	95	below_threshold
Fusobacterium gonidiaformans	strain=ATCC 25563	GCA_003019695.1	849	849	type	True	76.4724	51	530	95	below_threshold
Psychrilyobacter atlanticus	strain=DSM 19335	GCA_000426625.1	271091	271091	type	True	75.8357	72	530	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	74.9692	54	530	95	below_threshold
Tepiditoga spiralis	strain=sy52	GCA_014701195.1	2108365	2108365	type	True	74.6399	63	530	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 22:45:52,166] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17190/tc_result.tsv
[2023-03-16 22:45:52,166] [INFO] ===== Taxonomy check completed =====
[2023-03-16 22:45:52,166] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 22:45:52,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc22a480d-ecfb-4c12-8c16-a35f71a8e187/dqc_reference/checkm_data
[2023-03-16 22:45:52,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 22:45:52,170] [INFO] Task started: CheckM
[2023-03-16 22:45:52,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17190/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17190/checkm_input OceanDNA-b17190/checkm_result
[2023-03-16 22:46:16,780] [INFO] Task succeeded: CheckM
[2023-03-16 22:46:16,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 5.30%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 22:46:16,783] [INFO] ===== Completeness check finished =====
[2023-03-16 22:46:16,783] [INFO] ===== Start GTDB Search =====
[2023-03-16 22:46:16,783] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17190/markers.fasta)
[2023-03-16 22:46:16,783] [INFO] Task started: Blastn
[2023-03-16 22:46:16,783] [INFO] Running command: blastn -query OceanDNA-b17190/markers.fasta -db /var/lib/cwl/stgc22a480d-ecfb-4c12-8c16-a35f71a8e187/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17190/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:46:17,475] [INFO] Task succeeded: Blastn
[2023-03-16 22:46:17,476] [INFO] Selected 14 target genomes.
[2023-03-16 22:46:17,476] [INFO] Target genome list was writen to OceanDNA-b17190/target_genomes_gtdb.txt
[2023-03-16 22:46:17,785] [INFO] Task started: fastANI
[2023-03-16 22:46:17,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg86ad4d74-d0f4-4543-af2d-1fb55593fe47/OceanDNA-b17190.fa --refList OceanDNA-b17190/target_genomes_gtdb.txt --output OceanDNA-b17190/fastani_result_gtdb.tsv --threads 1
[2023-03-16 22:46:23,901] [INFO] Task succeeded: fastANI
[2023-03-16 22:46:23,909] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 22:46:23,909] [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_900167275.1	s__Cetobacterium ceti	97.0269	496	530	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014250685.1	s__Cetobacterium sp014250685	78.2793	208	530	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905216205.1	s__Cetobacterium_A sp905216205	77.9877	197	530	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014250675.1	s__Cetobacterium_A sp014250675	77.9011	168	530	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000479045.1	s__Cetobacterium_A somerae	77.7278	207	530	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	99.23	98.47	0.92	0.85	3	-
GCA_019012925.1	s__Fusobacterium_A sp019012925	77.7087	107	530	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799075.1	s__Cetobacterium_A sp000799075	77.5675	164	530	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	98.72	98.42	0.82	0.77	3	-
GCF_016900045.1	s__Fusobacterium_A sp900549465	77.5251	123	530	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	98.59	98.37	0.86	0.84	6	-
GCA_905193685.1	s__Fusobacterium_A sp900555485	77.5013	146	530	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900683735.1	s__Fusobacterium_A ulcerans_A	77.071	147	530	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	98.86	98.73	0.94	0.93	4	-
GCA_017984315.1	s__JAGNZR01 sp017984315	76.9076	84	530	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__JAGNZR01	95.0	99.31	99.23	0.88	0.86	3	-
GCA_900545035.1	s__Fusobacterium_B sp900545035	75.7026	59	530	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938425.1	s__JAFGUR01 sp016938425	75.5463	57	530	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__JAFGUR01	95.0	99.62	99.62	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-16 22:46:23,909] [INFO] GTDB search result was written to OceanDNA-b17190/result_gtdb.tsv
[2023-03-16 22:46:23,909] [INFO] ===== GTDB Search completed =====
[2023-03-16 22:46:23,911] [INFO] DFAST_QC result json was written to OceanDNA-b17190/dqc_result.json
[2023-03-16 22:46:23,911] [INFO] DFAST_QC completed!
[2023-03-16 22:46:23,911] [INFO] Total running time: 0h0m49s