[2023-03-16 11:12:36,930] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:12:36,930] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:12:36,930] [INFO] DQC Reference Directory: /var/lib/cwl/stg20a3290d-34d5-437b-9187-5151552ea615/dqc_reference
[2023-03-16 11:12:38,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:12:38,203] [INFO] Task started: Prodigal
[2023-03-16 11:12:38,203] [INFO] Running command: cat /var/lib/cwl/stg03108b2e-dd27-4b90-b82a-edbe5c2df04e/OceanDNA-b42884.fa | prodigal -d OceanDNA-b42884/cds.fna -a OceanDNA-b42884/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:12:43,959] [INFO] Task succeeded: Prodigal
[2023-03-16 11:12:43,960] [INFO] Task started: HMMsearch
[2023-03-16 11:12:43,960] [INFO] Running command: hmmsearch --tblout OceanDNA-b42884/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20a3290d-34d5-437b-9187-5151552ea615/dqc_reference/reference_markers.hmm OceanDNA-b42884/protein.faa > /dev/null
[2023-03-16 11:12:44,141] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:12:44,142] [INFO] Found 6/6 markers.
[2023-03-16 11:12:44,152] [INFO] Query marker FASTA was written to OceanDNA-b42884/markers.fasta
[2023-03-16 11:12:44,171] [INFO] Task started: Blastn
[2023-03-16 11:12:44,172] [INFO] Running command: blastn -query OceanDNA-b42884/markers.fasta -db /var/lib/cwl/stg20a3290d-34d5-437b-9187-5151552ea615/dqc_reference/reference_markers.fasta -out OceanDNA-b42884/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:12:44,817] [INFO] Task succeeded: Blastn
[2023-03-16 11:12:44,818] [INFO] Selected 27 target genomes.
[2023-03-16 11:12:44,818] [INFO] Target genome list was writen to OceanDNA-b42884/target_genomes.txt
[2023-03-16 11:12:44,829] [INFO] Task started: fastANI
[2023-03-16 11:12:44,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg03108b2e-dd27-4b90-b82a-edbe5c2df04e/OceanDNA-b42884.fa --refList OceanDNA-b42884/target_genomes.txt --output OceanDNA-b42884/fastani_result.tsv --threads 1
[2023-03-16 11:13:08,156] [INFO] Task succeeded: fastANI
[2023-03-16 11:13:08,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20a3290d-34d5-437b-9187-5151552ea615/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:13:08,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20a3290d-34d5-437b-9187-5151552ea615/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:13:08,160] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:13:08,160] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 11:13:08,160] [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
Candidatus Thioglobus autotrophicus	strain=EF1	GCA_001293165.1	1705394	1705394	type	True	78.5608	135	340	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:13:08,161] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42884/tc_result.tsv
[2023-03-16 11:13:08,161] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:13:08,161] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:13:08,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20a3290d-34d5-437b-9187-5151552ea615/dqc_reference/checkm_data
[2023-03-16 11:13:08,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:13:08,165] [INFO] Task started: CheckM
[2023-03-16 11:13:08,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42884/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42884/checkm_input OceanDNA-b42884/checkm_result
[2023-03-16 11:13:30,418] [INFO] Task succeeded: CheckM
[2023-03-16 11:13:30,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:13:30,422] [INFO] ===== Completeness check finished =====
[2023-03-16 11:13:30,422] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:13:30,422] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42884/markers.fasta)
[2023-03-16 11:13:30,423] [INFO] Task started: Blastn
[2023-03-16 11:13:30,423] [INFO] Running command: blastn -query OceanDNA-b42884/markers.fasta -db /var/lib/cwl/stg20a3290d-34d5-437b-9187-5151552ea615/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42884/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:13:31,497] [INFO] Task succeeded: Blastn
[2023-03-16 11:13:31,499] [INFO] Selected 16 target genomes.
[2023-03-16 11:13:31,499] [INFO] Target genome list was writen to OceanDNA-b42884/target_genomes_gtdb.txt
[2023-03-16 11:13:31,629] [INFO] Task started: fastANI
[2023-03-16 11:13:31,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg03108b2e-dd27-4b90-b82a-edbe5c2df04e/OceanDNA-b42884.fa --refList OceanDNA-b42884/target_genomes_gtdb.txt --output OceanDNA-b42884/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:13:36,931] [INFO] Task succeeded: fastANI
[2023-03-16 11:13:36,939] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 11:13:36,939] [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_000205985.2	s__SUP05 sp000205985	99.2161	265	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__SUP05	95.0	99.29	99.11	0.83	0.80	14	conclusive
GCA_003489145.1	s__UBA2013 sp003489145	79.8025	156	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	99.21	98.78	0.83	0.78	42	-
GCA_018648985.1	s__UBA2013 sp018648985	79.6407	155	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845205.1	s__UBA2013 sp016845205	79.2803	170	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335045.1	s__UBA2013 sp002335045	79.1479	186	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	98.42	96.96	0.95	0.94	3	-
GCA_003978285.1	s__UBA2013 sp003978285	78.9187	114	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978185.1	s__UBA2013 sp003978185	78.7961	98	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293165.1	s__Thioglobus autotrophicus	78.5608	135	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012963565.1	s__DTVJ01 sp012963565	78.2255	134	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__DTVJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384345.1	s__Thioglobus pontius	77.9899	141	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.87	99.85	0.90	0.85	3	-
GCF_900128515.1	s__Thioglobus sp900128515	77.9597	130	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.64	99.26	0.90	0.80	8	-
GCF_001298715.1	s__Thiodubiliella sp001298715	77.6401	92	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thiodubiliella	95.0	98.96	97.97	0.90	0.82	38	-
GCF_900128535.1	s__Thiodubiliella sp900128535	77.1827	118	340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thiodubiliella	95.0	98.14	96.23	0.87	0.79	15	-
--------------------------------------------------------------------------------
[2023-03-16 11:13:36,940] [INFO] GTDB search result was written to OceanDNA-b42884/result_gtdb.tsv
[2023-03-16 11:13:36,940] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:13:36,942] [INFO] DFAST_QC result json was written to OceanDNA-b42884/dqc_result.json
[2023-03-16 11:13:36,942] [INFO] DFAST_QC completed!
[2023-03-16 11:13:36,942] [INFO] Total running time: 0h1m0s