[2023-03-18 10:15:15,038] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:15:15,039] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:15:15,039] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a8a8138-1bd3-40ed-a087-e56cf1d158f3/dqc_reference
[2023-03-18 10:15:16,220] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:15:16,221] [INFO] Task started: Prodigal
[2023-03-18 10:15:16,221] [INFO] Running command: cat /var/lib/cwl/stgea529859-7657-473b-a412-c8c3f2349918/OceanDNA-b14430.fa | prodigal -d OceanDNA-b14430/cds.fna -a OceanDNA-b14430/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:15:21,288] [INFO] Task succeeded: Prodigal
[2023-03-18 10:15:21,288] [INFO] Task started: HMMsearch
[2023-03-18 10:15:21,289] [INFO] Running command: hmmsearch --tblout OceanDNA-b14430/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a8a8138-1bd3-40ed-a087-e56cf1d158f3/dqc_reference/reference_markers.hmm OceanDNA-b14430/protein.faa > /dev/null
[2023-03-18 10:15:21,481] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:15:21,482] [INFO] Found 6/6 markers.
[2023-03-18 10:15:21,490] [INFO] Query marker FASTA was written to OceanDNA-b14430/markers.fasta
[2023-03-18 10:15:21,492] [INFO] Task started: Blastn
[2023-03-18 10:15:21,492] [INFO] Running command: blastn -query OceanDNA-b14430/markers.fasta -db /var/lib/cwl/stg9a8a8138-1bd3-40ed-a087-e56cf1d158f3/dqc_reference/reference_markers.fasta -out OceanDNA-b14430/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:15:21,985] [INFO] Task succeeded: Blastn
[2023-03-18 10:15:21,986] [INFO] Selected 12 target genomes.
[2023-03-18 10:15:21,986] [INFO] Target genome list was writen to OceanDNA-b14430/target_genomes.txt
[2023-03-18 10:15:21,995] [INFO] Task started: fastANI
[2023-03-18 10:15:21,996] [INFO] Running command: fastANI --query /var/lib/cwl/stgea529859-7657-473b-a412-c8c3f2349918/OceanDNA-b14430.fa --refList OceanDNA-b14430/target_genomes.txt --output OceanDNA-b14430/fastani_result.tsv --threads 1
[2023-03-18 10:15:25,866] [INFO] Task succeeded: fastANI
[2023-03-18 10:15:25,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a8a8138-1bd3-40ed-a087-e56cf1d158f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:15:25,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a8a8138-1bd3-40ed-a087-e56cf1d158f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:15:25,867] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:15:25,867] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:15:25,867] [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
--------------------------------------------------------------------------------
[2023-03-18 10:15:25,867] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14430/tc_result.tsv
[2023-03-18 10:15:25,867] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:15:25,867] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:15:25,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a8a8138-1bd3-40ed-a087-e56cf1d158f3/dqc_reference/checkm_data
[2023-03-18 10:15:25,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:15:25,873] [INFO] Task started: CheckM
[2023-03-18 10:15:25,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14430/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14430/checkm_input OceanDNA-b14430/checkm_result
[2023-03-18 10:15:44,550] [INFO] Task succeeded: CheckM
[2023-03-18 10:15:44,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:15:44,551] [INFO] ===== Completeness check finished =====
[2023-03-18 10:15:44,552] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:15:44,552] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14430/markers.fasta)
[2023-03-18 10:15:44,553] [INFO] Task started: Blastn
[2023-03-18 10:15:44,553] [INFO] Running command: blastn -query OceanDNA-b14430/markers.fasta -db /var/lib/cwl/stg9a8a8138-1bd3-40ed-a087-e56cf1d158f3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14430/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:15:45,259] [INFO] Task succeeded: Blastn
[2023-03-18 10:15:45,260] [INFO] Selected 12 target genomes.
[2023-03-18 10:15:45,260] [INFO] Target genome list was writen to OceanDNA-b14430/target_genomes_gtdb.txt
[2023-03-18 10:15:45,270] [INFO] Task started: fastANI
[2023-03-18 10:15:45,270] [INFO] Running command: fastANI --query /var/lib/cwl/stgea529859-7657-473b-a412-c8c3f2349918/OceanDNA-b14430.fa --refList OceanDNA-b14430/target_genomes_gtdb.txt --output OceanDNA-b14430/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:15:48,873] [INFO] Task succeeded: fastANI
[2023-03-18 10:15:48,877] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:15:48,877] [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_002708145.1	s__GCA-002708145 sp002708145	90.0143	273	337	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002708145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714425.1	s__GCA-002708145 sp002714425	82.1614	282	337	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002708145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728715.1	s__GCA-002708145 sp002728715	82.0159	257	337	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002708145	95.0	98.77	97.83	0.89	0.87	3	-
GCA_002712125.1	s__GCA-002708145 sp002712125	81.2956	258	337	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002708145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:15:48,877] [INFO] GTDB search result was written to OceanDNA-b14430/result_gtdb.tsv
[2023-03-18 10:15:48,877] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:15:48,878] [INFO] DFAST_QC result json was written to OceanDNA-b14430/dqc_result.json
[2023-03-18 10:15:48,878] [INFO] DFAST_QC completed!
[2023-03-18 10:15:48,878] [INFO] Total running time: 0h0m34s