[2023-03-16 16:43:21,786] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:43:21,786] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:43:21,786] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b19ea59-c526-4199-b4b9-15caca54d5dc/dqc_reference
[2023-03-16 16:43:24,605] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:43:24,606] [INFO] Task started: Prodigal
[2023-03-16 16:43:24,606] [INFO] Running command: cat /var/lib/cwl/stgc29a0e93-eb32-480b-9b9d-b565bb0931eb/OceanDNA-b43052.fa | prodigal -d OceanDNA-b43052/cds.fna -a OceanDNA-b43052/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:43:29,800] [INFO] Task succeeded: Prodigal
[2023-03-16 16:43:29,800] [INFO] Task started: HMMsearch
[2023-03-16 16:43:29,800] [INFO] Running command: hmmsearch --tblout OceanDNA-b43052/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b19ea59-c526-4199-b4b9-15caca54d5dc/dqc_reference/reference_markers.hmm OceanDNA-b43052/protein.faa > /dev/null
[2023-03-16 16:43:29,984] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:43:29,984] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc29a0e93-eb32-480b-9b9d-b565bb0931eb/OceanDNA-b43052.fa]
[2023-03-16 16:43:29,995] [INFO] Query marker FASTA was written to OceanDNA-b43052/markers.fasta
[2023-03-16 16:43:29,995] [INFO] Task started: Blastn
[2023-03-16 16:43:29,995] [INFO] Running command: blastn -query OceanDNA-b43052/markers.fasta -db /var/lib/cwl/stg6b19ea59-c526-4199-b4b9-15caca54d5dc/dqc_reference/reference_markers.fasta -out OceanDNA-b43052/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:43:30,517] [INFO] Task succeeded: Blastn
[2023-03-16 16:43:30,518] [INFO] Selected 11 target genomes.
[2023-03-16 16:43:30,518] [INFO] Target genome list was writen to OceanDNA-b43052/target_genomes.txt
[2023-03-16 16:43:30,526] [INFO] Task started: fastANI
[2023-03-16 16:43:30,526] [INFO] Running command: fastANI --query /var/lib/cwl/stgc29a0e93-eb32-480b-9b9d-b565bb0931eb/OceanDNA-b43052.fa --refList OceanDNA-b43052/target_genomes.txt --output OceanDNA-b43052/fastani_result.tsv --threads 1
[2023-03-16 16:43:37,723] [INFO] Task succeeded: fastANI
[2023-03-16 16:43:37,723] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b19ea59-c526-4199-b4b9-15caca54d5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:43:37,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b19ea59-c526-4199-b4b9-15caca54d5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:43:37,778] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:43:37,778] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:43:37,779] [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 Pseudothioglobus singularis	strain=PS1	GCA_001281385.1	1427364	1427364	type	True	85.4012	220	255	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:43:37,779] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43052/tc_result.tsv
[2023-03-16 16:43:37,779] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:43:37,779] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:43:37,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b19ea59-c526-4199-b4b9-15caca54d5dc/dqc_reference/checkm_data
[2023-03-16 16:43:37,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:43:37,784] [INFO] Task started: CheckM
[2023-03-16 16:43:37,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43052/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43052/checkm_input OceanDNA-b43052/checkm_result
[2023-03-16 16:44:03,390] [INFO] Task succeeded: CheckM
[2023-03-16 16:44:03,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.67%
Contamintation: 3.12%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 16:44:03,392] [INFO] ===== Completeness check finished =====
[2023-03-16 16:44:03,392] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:44:03,392] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43052/markers.fasta)
[2023-03-16 16:44:03,393] [INFO] Task started: Blastn
[2023-03-16 16:44:03,393] [INFO] Running command: blastn -query OceanDNA-b43052/markers.fasta -db /var/lib/cwl/stg6b19ea59-c526-4199-b4b9-15caca54d5dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43052/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:44:04,135] [INFO] Task succeeded: Blastn
[2023-03-16 16:44:04,136] [INFO] Selected 7 target genomes.
[2023-03-16 16:44:04,136] [INFO] Target genome list was writen to OceanDNA-b43052/target_genomes_gtdb.txt
[2023-03-16 16:44:04,144] [INFO] Task started: fastANI
[2023-03-16 16:44:04,144] [INFO] Running command: fastANI --query /var/lib/cwl/stgc29a0e93-eb32-480b-9b9d-b565bb0931eb/OceanDNA-b43052.fa --refList OceanDNA-b43052/target_genomes_gtdb.txt --output OceanDNA-b43052/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:44:06,071] [INFO] Task succeeded: fastANI
[2023-03-16 16:44:06,077] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:44:06,077] [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_902513495.1	s__Pseudothioglobus sp902513495	98.1505	161	255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.65	97.05	0.53	0.51	3	conclusive
GCA_002711905.1	s__Pseudothioglobus sp002711905	85.7455	131	255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.25	97.13	0.60	0.55	8	-
GCF_001281385.1	s__Pseudothioglobus singularis	85.4012	220	255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	95.87	0.84	0.66	7	-
GCA_902512305.1	s__Pseudothioglobus sp902512305	80.6002	159	255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.03	95.27	0.77	0.74	5	-
GCA_902509905.1	s__Pseudothioglobus sp902509905	79.5989	137	255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.83	95.81	0.73	0.73	3	-
GCA_001628405.1	s__Pseudothioglobus sp001628405	78.9894	136	255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.86	96.69	0.86	0.83	3	-
--------------------------------------------------------------------------------
[2023-03-16 16:44:06,078] [INFO] GTDB search result was written to OceanDNA-b43052/result_gtdb.tsv
[2023-03-16 16:44:06,078] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:44:06,079] [INFO] DFAST_QC result json was written to OceanDNA-b43052/dqc_result.json
[2023-03-16 16:44:06,079] [INFO] DFAST_QC completed!
[2023-03-16 16:44:06,079] [INFO] Total running time: 0h0m44s