[2023-03-16 12:37:44,843] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:37:44,843] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:37:44,843] [INFO] DQC Reference Directory: /var/lib/cwl/stge5cbdbc2-bbff-4ae1-91e9-fd7cf7cb8d56/dqc_reference
[2023-03-16 12:37:45,956] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:37:45,956] [INFO] Task started: Prodigal
[2023-03-16 12:37:45,956] [INFO] Running command: cat /var/lib/cwl/stg113dd778-8e9f-4ab0-92d8-64d87ae4cdc0/OceanDNA-b12661.fa | prodigal -d OceanDNA-b12661/cds.fna -a OceanDNA-b12661/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:38:02,619] [INFO] Task succeeded: Prodigal
[2023-03-16 12:38:02,619] [INFO] Task started: HMMsearch
[2023-03-16 12:38:02,619] [INFO] Running command: hmmsearch --tblout OceanDNA-b12661/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5cbdbc2-bbff-4ae1-91e9-fd7cf7cb8d56/dqc_reference/reference_markers.hmm OceanDNA-b12661/protein.faa > /dev/null
[2023-03-16 12:38:02,790] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:38:02,790] [INFO] Found 6/6 markers.
[2023-03-16 12:38:02,806] [INFO] Query marker FASTA was written to OceanDNA-b12661/markers.fasta
[2023-03-16 12:38:02,807] [INFO] Task started: Blastn
[2023-03-16 12:38:02,807] [INFO] Running command: blastn -query OceanDNA-b12661/markers.fasta -db /var/lib/cwl/stge5cbdbc2-bbff-4ae1-91e9-fd7cf7cb8d56/dqc_reference/reference_markers.fasta -out OceanDNA-b12661/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:38:03,338] [INFO] Task succeeded: Blastn
[2023-03-16 12:38:03,339] [INFO] Selected 27 target genomes.
[2023-03-16 12:38:03,339] [INFO] Target genome list was writen to OceanDNA-b12661/target_genomes.txt
[2023-03-16 12:38:03,352] [INFO] Task started: fastANI
[2023-03-16 12:38:03,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg113dd778-8e9f-4ab0-92d8-64d87ae4cdc0/OceanDNA-b12661.fa --refList OceanDNA-b12661/target_genomes.txt --output OceanDNA-b12661/fastani_result.tsv --threads 1
[2023-03-16 12:38:19,467] [INFO] Task succeeded: fastANI
[2023-03-16 12:38:19,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5cbdbc2-bbff-4ae1-91e9-fd7cf7cb8d56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:38:19,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5cbdbc2-bbff-4ae1-91e9-fd7cf7cb8d56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:38:19,471] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:38:19,471] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 12:38:19,471] [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
Acidiluteibacter ferrifornacis	strain=S-15	GCA_009909615.1	2692424	2692424	type	True	76.0206	55	817	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 12:38:19,471] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12661/tc_result.tsv
[2023-03-16 12:38:19,471] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:38:19,471] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:38:19,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5cbdbc2-bbff-4ae1-91e9-fd7cf7cb8d56/dqc_reference/checkm_data
[2023-03-16 12:38:19,472] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:38:19,477] [INFO] Task started: CheckM
[2023-03-16 12:38:19,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12661/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12661/checkm_input OceanDNA-b12661/checkm_result
[2023-03-16 12:39:15,931] [INFO] Task succeeded: CheckM
[2023-03-16 12:39:15,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 12:39:15,934] [INFO] ===== Completeness check finished =====
[2023-03-16 12:39:15,934] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:39:15,934] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12661/markers.fasta)
[2023-03-16 12:39:15,935] [INFO] Task started: Blastn
[2023-03-16 12:39:15,935] [INFO] Running command: blastn -query OceanDNA-b12661/markers.fasta -db /var/lib/cwl/stge5cbdbc2-bbff-4ae1-91e9-fd7cf7cb8d56/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12661/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:39:16,761] [INFO] Task succeeded: Blastn
[2023-03-16 12:39:16,762] [INFO] Selected 19 target genomes.
[2023-03-16 12:39:16,762] [INFO] Target genome list was writen to OceanDNA-b12661/target_genomes_gtdb.txt
[2023-03-16 12:39:16,960] [INFO] Task started: fastANI
[2023-03-16 12:39:16,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg113dd778-8e9f-4ab0-92d8-64d87ae4cdc0/OceanDNA-b12661.fa --refList OceanDNA-b12661/target_genomes_gtdb.txt --output OceanDNA-b12661/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:39:33,163] [INFO] Task succeeded: fastANI
[2023-03-16 12:39:33,167] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 12:39:33,167] [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_018608405.1	s__NORP294 sp018608405	99.8235	794	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__NORP294	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905479325.1	s__NORP294 sp905479325	79.0754	362	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__NORP294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182175.1	s__NORP294 sp905182175	77.9762	304	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__NORP294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763995.1	s__NORP294 sp016763995	77.3679	148	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__NORP294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013112545.1	s__BCD18 sp013112545	76.7616	93	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BCD18	95.0	99.98	99.95	0.99	0.99	3	-
GCA_002415785.1	s__UBA5081 sp002415785	76.2899	72	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__UBA5081	95.0	99.97	99.97	0.98	0.96	4	-
--------------------------------------------------------------------------------
[2023-03-16 12:39:33,167] [INFO] GTDB search result was written to OceanDNA-b12661/result_gtdb.tsv
[2023-03-16 12:39:33,167] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:39:33,168] [INFO] DFAST_QC result json was written to OceanDNA-b12661/dqc_result.json
[2023-03-16 12:39:33,168] [INFO] DFAST_QC completed!
[2023-03-16 12:39:33,168] [INFO] Total running time: 0h1m48s