[2023-03-19 00:04:59,408] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:04:59,408] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:04:59,408] [INFO] DQC Reference Directory: /var/lib/cwl/stge7495453-beed-49ff-acd5-0fac0157f245/dqc_reference
[2023-03-19 00:05:00,513] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:05:00,514] [INFO] Task started: Prodigal
[2023-03-19 00:05:00,514] [INFO] Running command: cat /var/lib/cwl/stgef9ad008-9e62-46d5-bb12-93853d924921/OceanDNA-b32365.fa | prodigal -d OceanDNA-b32365/cds.fna -a OceanDNA-b32365/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:05:07,045] [INFO] Task succeeded: Prodigal
[2023-03-19 00:05:07,046] [INFO] Task started: HMMsearch
[2023-03-19 00:05:07,046] [INFO] Running command: hmmsearch --tblout OceanDNA-b32365/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7495453-beed-49ff-acd5-0fac0157f245/dqc_reference/reference_markers.hmm OceanDNA-b32365/protein.faa > /dev/null
[2023-03-19 00:05:07,197] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:05:07,197] [INFO] Found 6/6 markers.
[2023-03-19 00:05:07,209] [INFO] Query marker FASTA was written to OceanDNA-b32365/markers.fasta
[2023-03-19 00:05:07,210] [INFO] Task started: Blastn
[2023-03-19 00:05:07,210] [INFO] Running command: blastn -query OceanDNA-b32365/markers.fasta -db /var/lib/cwl/stge7495453-beed-49ff-acd5-0fac0157f245/dqc_reference/reference_markers.fasta -out OceanDNA-b32365/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:05:07,751] [INFO] Task succeeded: Blastn
[2023-03-19 00:05:07,752] [INFO] Selected 18 target genomes.
[2023-03-19 00:05:07,752] [INFO] Target genome list was writen to OceanDNA-b32365/target_genomes.txt
[2023-03-19 00:05:07,762] [INFO] Task started: fastANI
[2023-03-19 00:05:07,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgef9ad008-9e62-46d5-bb12-93853d924921/OceanDNA-b32365.fa --refList OceanDNA-b32365/target_genomes.txt --output OceanDNA-b32365/fastani_result.tsv --threads 1
[2023-03-19 00:05:14,884] [INFO] Task succeeded: fastANI
[2023-03-19 00:05:14,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7495453-beed-49ff-acd5-0fac0157f245/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:05:14,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7495453-beed-49ff-acd5-0fac0157f245/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:05:14,884] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:05:14,884] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:05:14,885] [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
--------------------------------------------------------------------------------
[2023-03-19 00:05:14,885] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32365/tc_result.tsv
[2023-03-19 00:05:14,885] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:05:14,885] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:05:14,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7495453-beed-49ff-acd5-0fac0157f245/dqc_reference/checkm_data
[2023-03-19 00:05:14,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:05:14,891] [INFO] Task started: CheckM
[2023-03-19 00:05:14,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32365/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32365/checkm_input OceanDNA-b32365/checkm_result
[2023-03-19 00:05:36,175] [INFO] Task succeeded: CheckM
[2023-03-19 00:05:36,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:05:36,177] [INFO] ===== Completeness check finished =====
[2023-03-19 00:05:36,177] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:05:36,177] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32365/markers.fasta)
[2023-03-19 00:05:36,177] [INFO] Task started: Blastn
[2023-03-19 00:05:36,178] [INFO] Running command: blastn -query OceanDNA-b32365/markers.fasta -db /var/lib/cwl/stge7495453-beed-49ff-acd5-0fac0157f245/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32365/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:05:37,068] [INFO] Task succeeded: Blastn
[2023-03-19 00:05:37,069] [INFO] Selected 21 target genomes.
[2023-03-19 00:05:37,069] [INFO] Target genome list was writen to OceanDNA-b32365/target_genomes_gtdb.txt
[2023-03-19 00:05:37,085] [INFO] Task started: fastANI
[2023-03-19 00:05:37,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgef9ad008-9e62-46d5-bb12-93853d924921/OceanDNA-b32365.fa --refList OceanDNA-b32365/target_genomes_gtdb.txt --output OceanDNA-b32365/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:05:41,409] [INFO] Task succeeded: fastANI
[2023-03-19 00:05:41,413] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:05:41,414] [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_002684605.1	s__TMED109 sp002684605	99.4016	380	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015660425.1	s__TMED109 sp015660425	81.5648	184	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171375.1	s__TMED109 sp002171375	77.9972	176	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	98.96	97.53	0.84	0.73	4	-
GCA_002937655.1	s__TMED109 sp002937655	77.5318	182	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	99.81	99.81	0.91	0.91	2	-
GCA_002720535.1	s__TMED109 sp002720535	77.4379	187	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	95.89	95.27	0.82	0.81	3	-
GCA_002715265.1	s__GCA-002727615 sp002715265	76.3152	116	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__GCA-002727615	95.0	98.23	98.23	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-19 00:05:41,414] [INFO] GTDB search result was written to OceanDNA-b32365/result_gtdb.tsv
[2023-03-19 00:05:41,415] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:05:41,416] [INFO] DFAST_QC result json was written to OceanDNA-b32365/dqc_result.json
[2023-03-19 00:05:41,416] [INFO] DFAST_QC completed!
[2023-03-19 00:05:41,416] [INFO] Total running time: 0h0m42s