[2023-03-15 07:52:40,252] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,252] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,252] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c3b7ae7-2742-44cb-abf8-933f3a6cb07c/dqc_reference
[2023-03-15 07:52:41,385] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,385] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,385] [INFO] Running command: cat /var/lib/cwl/stg38e88f25-f9e9-40ab-b144-7ae5cde91433/OceanDNA-b28266.fa | prodigal -d OceanDNA-b28266/cds.fna -a OceanDNA-b28266/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:52:47,891] [INFO] Task succeeded: Prodigal
[2023-03-15 07:52:47,892] [INFO] Task started: HMMsearch
[2023-03-15 07:52:47,892] [INFO] Running command: hmmsearch --tblout OceanDNA-b28266/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c3b7ae7-2742-44cb-abf8-933f3a6cb07c/dqc_reference/reference_markers.hmm OceanDNA-b28266/protein.faa > /dev/null
[2023-03-15 07:52:48,103] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:52:48,104] [INFO] Found 6/6 markers.
[2023-03-15 07:52:48,118] [INFO] Query marker FASTA was written to OceanDNA-b28266/markers.fasta
[2023-03-15 07:52:48,118] [INFO] Task started: Blastn
[2023-03-15 07:52:48,118] [INFO] Running command: blastn -query OceanDNA-b28266/markers.fasta -db /var/lib/cwl/stg5c3b7ae7-2742-44cb-abf8-933f3a6cb07c/dqc_reference/reference_markers.fasta -out OceanDNA-b28266/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:52:48,670] [INFO] Task succeeded: Blastn
[2023-03-15 07:52:48,670] [INFO] Selected 21 target genomes.
[2023-03-15 07:52:48,671] [INFO] Target genome list was writen to OceanDNA-b28266/target_genomes.txt
[2023-03-15 07:52:48,683] [INFO] Task started: fastANI
[2023-03-15 07:52:48,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg38e88f25-f9e9-40ab-b144-7ae5cde91433/OceanDNA-b28266.fa --refList OceanDNA-b28266/target_genomes.txt --output OceanDNA-b28266/fastani_result.tsv --threads 1
[2023-03-15 07:52:57,964] [INFO] Task succeeded: fastANI
[2023-03-15 07:52:57,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c3b7ae7-2742-44cb-abf8-933f3a6cb07c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:52:57,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c3b7ae7-2742-44cb-abf8-933f3a6cb07c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:52:57,965] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:52:57,965] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:52:57,965] [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
--------------------------------------------------------------------------------
[2023-03-15 07:52:57,965] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28266/tc_result.tsv
[2023-03-15 07:52:57,965] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:52:57,965] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:52:57,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c3b7ae7-2742-44cb-abf8-933f3a6cb07c/dqc_reference/checkm_data
[2023-03-15 07:52:57,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:52:57,972] [INFO] Task started: CheckM
[2023-03-15 07:52:57,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28266/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28266/checkm_input OceanDNA-b28266/checkm_result
[2023-03-15 07:53:20,476] [INFO] Task succeeded: CheckM
[2023-03-15 07:53:20,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.37%
Contamintation: 7.70%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2023-03-15 07:53:20,479] [INFO] ===== Completeness check finished =====
[2023-03-15 07:53:20,479] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:53:20,479] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28266/markers.fasta)
[2023-03-15 07:53:20,479] [INFO] Task started: Blastn
[2023-03-15 07:53:20,479] [INFO] Running command: blastn -query OceanDNA-b28266/markers.fasta -db /var/lib/cwl/stg5c3b7ae7-2742-44cb-abf8-933f3a6cb07c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28266/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:21,370] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:21,371] [INFO] Selected 35 target genomes.
[2023-03-15 07:53:21,371] [INFO] Target genome list was writen to OceanDNA-b28266/target_genomes_gtdb.txt
[2023-03-15 07:53:21,450] [INFO] Task started: fastANI
[2023-03-15 07:53:21,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg38e88f25-f9e9-40ab-b144-7ae5cde91433/OceanDNA-b28266.fa --refList OceanDNA-b28266/target_genomes_gtdb.txt --output OceanDNA-b28266/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:53:31,902] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:31,904] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:53:31,904] [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_902600895.1	s__CACKLF01 sp902600895	84.3652	98	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACKLF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902533625.1	s__CACKLF01 sp002725175	76.8805	55	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACKLF01	95.0	96.00	95.41	0.67	0.59	4	-
--------------------------------------------------------------------------------
[2023-03-15 07:53:31,904] [INFO] GTDB search result was written to OceanDNA-b28266/result_gtdb.tsv
[2023-03-15 07:53:31,905] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:53:31,905] [INFO] DFAST_QC result json was written to OceanDNA-b28266/dqc_result.json
[2023-03-15 07:53:31,905] [INFO] DFAST_QC completed!
[2023-03-15 07:53:31,905] [INFO] Total running time: 0h0m52s