[2023-03-17 02:45:48,876] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:45:48,876] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:45:48,876] [INFO] DQC Reference Directory: /var/lib/cwl/stg9170a5ca-e236-4152-bf45-4bf2432c567a/dqc_reference
[2023-03-17 02:45:50,399] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:45:50,399] [INFO] Task started: Prodigal
[2023-03-17 02:45:50,399] [INFO] Running command: cat /var/lib/cwl/stga862f349-c5fe-4f4e-b29f-3ac606565ece/OceanDNA-b36004.fa | prodigal -d OceanDNA-b36004/cds.fna -a OceanDNA-b36004/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:46:04,294] [INFO] Task succeeded: Prodigal
[2023-03-17 02:46:04,294] [INFO] Task started: HMMsearch
[2023-03-17 02:46:04,294] [INFO] Running command: hmmsearch --tblout OceanDNA-b36004/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9170a5ca-e236-4152-bf45-4bf2432c567a/dqc_reference/reference_markers.hmm OceanDNA-b36004/protein.faa > /dev/null
[2023-03-17 02:46:04,489] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:46:04,490] [INFO] Found 6/6 markers.
[2023-03-17 02:46:04,507] [INFO] Query marker FASTA was written to OceanDNA-b36004/markers.fasta
[2023-03-17 02:46:04,508] [INFO] Task started: Blastn
[2023-03-17 02:46:04,508] [INFO] Running command: blastn -query OceanDNA-b36004/markers.fasta -db /var/lib/cwl/stg9170a5ca-e236-4152-bf45-4bf2432c567a/dqc_reference/reference_markers.fasta -out OceanDNA-b36004/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:46:05,094] [INFO] Task succeeded: Blastn
[2023-03-17 02:46:05,095] [INFO] Selected 31 target genomes.
[2023-03-17 02:46:05,095] [INFO] Target genome list was writen to OceanDNA-b36004/target_genomes.txt
[2023-03-17 02:46:05,137] [INFO] Task started: fastANI
[2023-03-17 02:46:05,138] [INFO] Running command: fastANI --query /var/lib/cwl/stga862f349-c5fe-4f4e-b29f-3ac606565ece/OceanDNA-b36004.fa --refList OceanDNA-b36004/target_genomes.txt --output OceanDNA-b36004/fastani_result.tsv --threads 1
[2023-03-17 02:46:23,669] [INFO] Task succeeded: fastANI
[2023-03-17 02:46:23,670] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9170a5ca-e236-4152-bf45-4bf2432c567a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:46:23,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9170a5ca-e236-4152-bf45-4bf2432c567a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:46:23,673] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:46:23,673] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:46:23,673] [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
Methyloprofundus sedimenti	strain=WF1	GCA_002072955.1	1420851	1420851	type	True	79.8264	497	884	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:46:23,673] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36004/tc_result.tsv
[2023-03-17 02:46:23,673] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:46:23,673] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:46:23,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9170a5ca-e236-4152-bf45-4bf2432c567a/dqc_reference/checkm_data
[2023-03-17 02:46:23,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:46:23,867] [INFO] Task started: CheckM
[2023-03-17 02:46:23,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36004/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36004/checkm_input OceanDNA-b36004/checkm_result
[2023-03-17 02:47:01,730] [INFO] Task succeeded: CheckM
[2023-03-17 02:47:01,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:47:01,737] [INFO] ===== Completeness check finished =====
[2023-03-17 02:47:01,737] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:47:01,737] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36004/markers.fasta)
[2023-03-17 02:47:01,738] [INFO] Task started: Blastn
[2023-03-17 02:47:01,738] [INFO] Running command: blastn -query OceanDNA-b36004/markers.fasta -db /var/lib/cwl/stg9170a5ca-e236-4152-bf45-4bf2432c567a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36004/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:47:02,700] [INFO] Task succeeded: Blastn
[2023-03-17 02:47:02,702] [INFO] Selected 9 target genomes.
[2023-03-17 02:47:02,703] [INFO] Target genome list was writen to OceanDNA-b36004/target_genomes_gtdb.txt
[2023-03-17 02:47:02,728] [INFO] Task started: fastANI
[2023-03-17 02:47:02,728] [INFO] Running command: fastANI --query /var/lib/cwl/stga862f349-c5fe-4f4e-b29f-3ac606565ece/OceanDNA-b36004.fa --refList OceanDNA-b36004/target_genomes_gtdb.txt --output OceanDNA-b36004/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:47:09,185] [INFO] Task succeeded: fastANI
[2023-03-17 02:47:09,191] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:47:09,191] [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_012960135.1	s__Methyloprofundus sp012960135	97.9373	676	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	98.32	97.92	0.84	0.80	9	conclusive
GCF_002072955.1	s__Methyloprofundus sedimenti	79.8279	496	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002189065.1	s__Methyloprofundus sp002189065	79.5117	405	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138555.1	s__Methyloprofundus sp013138555	78.0136	224	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016592635.1	s__Methyloprofundus sp016592635	78.0074	218	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859465.1	s__Methyloprofundus sp014859465	77.465	208	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128525.1	s__Methyloprofundus sp900128525	77.442	193	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138595.1	s__Methyloprofundus sp013138595	77.0374	153	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:47:09,195] [INFO] GTDB search result was written to OceanDNA-b36004/result_gtdb.tsv
[2023-03-17 02:47:09,198] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:47:09,199] [INFO] DFAST_QC result json was written to OceanDNA-b36004/dqc_result.json
[2023-03-17 02:47:09,199] [INFO] DFAST_QC completed!
[2023-03-17 02:47:09,199] [INFO] Total running time: 0h1m20s