[2023-03-19 04:43:18,659] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,660] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,660] [INFO] DQC Reference Directory: /var/lib/cwl/stgeddb38d9-509a-4f29-b938-4e7eafdadfca/dqc_reference
[2023-03-19 04:43:19,812] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,812] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,812] [INFO] Running command: cat /var/lib/cwl/stgb9e7b356-1b04-4aaa-bd44-811b21520e97/OceanDNA-b6165.fa | prodigal -d OceanDNA-b6165/cds.fna -a OceanDNA-b6165/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:35,684] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:35,684] [INFO] Task started: HMMsearch
[2023-03-19 04:43:35,684] [INFO] Running command: hmmsearch --tblout OceanDNA-b6165/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeddb38d9-509a-4f29-b938-4e7eafdadfca/dqc_reference/reference_markers.hmm OceanDNA-b6165/protein.faa > /dev/null
[2023-03-19 04:43:35,866] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:35,867] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb9e7b356-1b04-4aaa-bd44-811b21520e97/OceanDNA-b6165.fa]
[2023-03-19 04:43:35,882] [INFO] Query marker FASTA was written to OceanDNA-b6165/markers.fasta
[2023-03-19 04:43:35,884] [INFO] Task started: Blastn
[2023-03-19 04:43:35,884] [INFO] Running command: blastn -query OceanDNA-b6165/markers.fasta -db /var/lib/cwl/stgeddb38d9-509a-4f29-b938-4e7eafdadfca/dqc_reference/reference_markers.fasta -out OceanDNA-b6165/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:36,425] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:36,426] [INFO] Selected 19 target genomes.
[2023-03-19 04:43:36,427] [INFO] Target genome list was writen to OceanDNA-b6165/target_genomes.txt
[2023-03-19 04:43:36,464] [INFO] Task started: fastANI
[2023-03-19 04:43:36,464] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9e7b356-1b04-4aaa-bd44-811b21520e97/OceanDNA-b6165.fa --refList OceanDNA-b6165/target_genomes.txt --output OceanDNA-b6165/fastani_result.tsv --threads 1
[2023-03-19 04:43:48,021] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:48,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeddb38d9-509a-4f29-b938-4e7eafdadfca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:43:48,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeddb38d9-509a-4f29-b938-4e7eafdadfca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:43:48,025] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:43:48,025] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:43:48,025] [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
Croceimicrobium hydrocarbonivorans	strain=A20-9	GCA_014524565.1	2761580	2761580	type	True	77.5222	150	740	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:43:48,025] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6165/tc_result.tsv
[2023-03-19 04:43:48,025] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:43:48,025] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:43:48,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeddb38d9-509a-4f29-b938-4e7eafdadfca/dqc_reference/checkm_data
[2023-03-19 04:43:48,026] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:43:48,032] [INFO] Task started: CheckM
[2023-03-19 04:43:48,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6165/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6165/checkm_input OceanDNA-b6165/checkm_result
[2023-03-19 04:44:30,679] [INFO] Task succeeded: CheckM
[2023-03-19 04:44:30,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:44:30,682] [INFO] ===== Completeness check finished =====
[2023-03-19 04:44:30,682] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:44:30,682] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6165/markers.fasta)
[2023-03-19 04:44:30,682] [INFO] Task started: Blastn
[2023-03-19 04:44:30,682] [INFO] Running command: blastn -query OceanDNA-b6165/markers.fasta -db /var/lib/cwl/stgeddb38d9-509a-4f29-b938-4e7eafdadfca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6165/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:44:31,449] [INFO] Task succeeded: Blastn
[2023-03-19 04:44:31,450] [INFO] Selected 24 target genomes.
[2023-03-19 04:44:31,450] [INFO] Target genome list was writen to OceanDNA-b6165/target_genomes_gtdb.txt
[2023-03-19 04:44:31,545] [INFO] Task started: fastANI
[2023-03-19 04:44:31,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9e7b356-1b04-4aaa-bd44-811b21520e97/OceanDNA-b6165.fa --refList OceanDNA-b6165/target_genomes_gtdb.txt --output OceanDNA-b6165/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:44:45,054] [INFO] Task succeeded: fastANI
[2023-03-19 04:44:45,058] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:44:45,058] [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_017795025.1	s__Croceimicrobium sp017795025	77.6209	127	740	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002501205.1	s__Croceimicrobium sp002501205	77.5123	140	740	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	99.91	99.91	0.95	0.95	2	-
GCF_014524565.1	s__Croceimicrobium hydrocarbonivorans	77.503	151	740	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401735.1	s__Croceimicrobium sp018401735	76.3667	110	740	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:44:45,059] [INFO] GTDB search result was written to OceanDNA-b6165/result_gtdb.tsv
[2023-03-19 04:44:45,059] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:44:45,059] [INFO] DFAST_QC result json was written to OceanDNA-b6165/dqc_result.json
[2023-03-19 04:44:45,059] [INFO] DFAST_QC completed!
[2023-03-19 04:44:45,059] [INFO] Total running time: 0h1m26s