[2023-03-17 05:59:13,004] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:59:13,004] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:59:13,004] [INFO] DQC Reference Directory: /var/lib/cwl/stg64f73e3d-7311-4de1-aa1a-cddd48a63c11/dqc_reference
[2023-03-17 05:59:14,108] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:59:14,108] [INFO] Task started: Prodigal
[2023-03-17 05:59:14,108] [INFO] Running command: cat /var/lib/cwl/stg2c3c751f-497c-49b6-9f48-7252e89f0708/OceanDNA-b43375.fa | prodigal -d OceanDNA-b43375/cds.fna -a OceanDNA-b43375/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:59:18,811] [INFO] Task succeeded: Prodigal
[2023-03-17 05:59:18,812] [INFO] Task started: HMMsearch
[2023-03-17 05:59:18,812] [INFO] Running command: hmmsearch --tblout OceanDNA-b43375/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64f73e3d-7311-4de1-aa1a-cddd48a63c11/dqc_reference/reference_markers.hmm OceanDNA-b43375/protein.faa > /dev/null
[2023-03-17 05:59:18,966] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:59:18,966] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2c3c751f-497c-49b6-9f48-7252e89f0708/OceanDNA-b43375.fa]
[2023-03-17 05:59:18,973] [INFO] Query marker FASTA was written to OceanDNA-b43375/markers.fasta
[2023-03-17 05:59:18,973] [INFO] Task started: Blastn
[2023-03-17 05:59:18,974] [INFO] Running command: blastn -query OceanDNA-b43375/markers.fasta -db /var/lib/cwl/stg64f73e3d-7311-4de1-aa1a-cddd48a63c11/dqc_reference/reference_markers.fasta -out OceanDNA-b43375/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:19,484] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:19,485] [INFO] Selected 17 target genomes.
[2023-03-17 05:59:19,485] [INFO] Target genome list was writen to OceanDNA-b43375/target_genomes.txt
[2023-03-17 05:59:19,493] [INFO] Task started: fastANI
[2023-03-17 05:59:19,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c3c751f-497c-49b6-9f48-7252e89f0708/OceanDNA-b43375.fa --refList OceanDNA-b43375/target_genomes.txt --output OceanDNA-b43375/fastani_result.tsv --threads 1
[2023-03-17 05:59:27,198] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:27,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64f73e3d-7311-4de1-aa1a-cddd48a63c11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:59:27,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64f73e3d-7311-4de1-aa1a-cddd48a63c11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:59:27,201] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:59:27,201] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:59:27,201] [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	82.7438	235	295	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:59:27,201] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43375/tc_result.tsv
[2023-03-17 05:59:27,201] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:59:27,201] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:59:27,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64f73e3d-7311-4de1-aa1a-cddd48a63c11/dqc_reference/checkm_data
[2023-03-17 05:59:27,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:59:27,204] [INFO] Task started: CheckM
[2023-03-17 05:59:27,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43375/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43375/checkm_input OceanDNA-b43375/checkm_result
[2023-03-17 05:59:44,911] [INFO] Task succeeded: CheckM
[2023-03-17 05:59:44,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:59:44,913] [INFO] ===== Completeness check finished =====
[2023-03-17 05:59:44,913] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:59:44,913] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43375/markers.fasta)
[2023-03-17 05:59:44,913] [INFO] Task started: Blastn
[2023-03-17 05:59:44,913] [INFO] Running command: blastn -query OceanDNA-b43375/markers.fasta -db /var/lib/cwl/stg64f73e3d-7311-4de1-aa1a-cddd48a63c11/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43375/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:45,607] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:45,607] [INFO] Selected 15 target genomes.
[2023-03-17 05:59:45,608] [INFO] Target genome list was writen to OceanDNA-b43375/target_genomes_gtdb.txt
[2023-03-17 05:59:45,640] [INFO] Task started: fastANI
[2023-03-17 05:59:45,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c3c751f-497c-49b6-9f48-7252e89f0708/OceanDNA-b43375.fa --refList OceanDNA-b43375/target_genomes_gtdb.txt --output OceanDNA-b43375/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:59:49,554] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:49,562] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:59:49,562] [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_001293165.1	s__Thioglobus autotrophicus	82.7438	235	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018644675.1	s__Thioglobus sp018644675	80.3746	199	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.74	99.56	0.96	0.91	16	-
GCA_014384345.1	s__Thioglobus pontius	79.0406	155	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.87	99.85	0.90	0.85	3	-
GCA_012963715.1	s__Thioglobus sp012963715	78.7213	132	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	97.05	95.18	0.84	0.80	5	-
GCA_900180385.1	s__Thioglobus sp900180385	78.6658	162	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128515.1	s__Thioglobus sp900128515	78.3804	146	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.64	99.26	0.90	0.80	8	-
GCA_016845205.1	s__UBA2013 sp016845205	77.8919	102	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002909145.1	s__Thioglobus_B perditus	77.7823	95	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001298715.1	s__Thiodubiliella sp001298715	77.2491	64	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thiodubiliella	95.0	98.96	97.97	0.90	0.82	38	-
GCA_000205985.2	s__SUP05 sp000205985	77.173	79	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__SUP05	95.0	99.29	99.11	0.83	0.80	14	-
GCF_900128535.1	s__Thiodubiliella sp900128535	77.1626	79	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thiodubiliella	95.0	98.14	96.23	0.87	0.79	15	-
GCA_013416635.1	s__Thiodubiliella endoseptemdiera	76.8444	64	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thiodubiliella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012963565.1	s__DTVJ01 sp012963565	76.7951	71	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__DTVJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:59:49,562] [INFO] GTDB search result was written to OceanDNA-b43375/result_gtdb.tsv
[2023-03-17 05:59:49,562] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:59:49,563] [INFO] DFAST_QC result json was written to OceanDNA-b43375/dqc_result.json
[2023-03-17 05:59:49,564] [INFO] DFAST_QC completed!
[2023-03-17 05:59:49,564] [INFO] Total running time: 0h0m37s