[2023-03-15 10:21:45,767] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:21:45,767] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:21:45,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bf96188-3ca8-44ff-a591-52c13c7372ab/dqc_reference
[2023-03-15 10:21:46,964] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:21:46,987] [INFO] Task started: Prodigal
[2023-03-15 10:21:46,987] [INFO] Running command: cat /var/lib/cwl/stg1c369c3f-8606-40c8-89ef-6771ba12ccea/OceanDNA-b17565.fa | prodigal -d OceanDNA-b17565/cds.fna -a OceanDNA-b17565/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:21:58,204] [INFO] Task succeeded: Prodigal
[2023-03-15 10:21:58,204] [INFO] Task started: HMMsearch
[2023-03-15 10:21:58,204] [INFO] Running command: hmmsearch --tblout OceanDNA-b17565/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bf96188-3ca8-44ff-a591-52c13c7372ab/dqc_reference/reference_markers.hmm OceanDNA-b17565/protein.faa > /dev/null
[2023-03-15 10:21:58,396] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:21:58,397] [INFO] Found 6/6 markers.
[2023-03-15 10:21:58,412] [INFO] Query marker FASTA was written to OceanDNA-b17565/markers.fasta
[2023-03-15 10:21:58,412] [INFO] Task started: Blastn
[2023-03-15 10:21:58,412] [INFO] Running command: blastn -query OceanDNA-b17565/markers.fasta -db /var/lib/cwl/stg1bf96188-3ca8-44ff-a591-52c13c7372ab/dqc_reference/reference_markers.fasta -out OceanDNA-b17565/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:21:58,916] [INFO] Task succeeded: Blastn
[2023-03-15 10:21:58,917] [INFO] Selected 5 target genomes.
[2023-03-15 10:21:58,917] [INFO] Target genome list was writen to OceanDNA-b17565/target_genomes.txt
[2023-03-15 10:21:58,920] [INFO] Task started: fastANI
[2023-03-15 10:21:58,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c369c3f-8606-40c8-89ef-6771ba12ccea/OceanDNA-b17565.fa --refList OceanDNA-b17565/target_genomes.txt --output OceanDNA-b17565/fastani_result.tsv --threads 1
[2023-03-15 10:22:01,636] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:01,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bf96188-3ca8-44ff-a591-52c13c7372ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:22:01,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bf96188-3ca8-44ff-a591-52c13c7372ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:22:01,637] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:22:01,637] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:22:01,637] [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 10:22:01,637] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17565/tc_result.tsv
[2023-03-15 10:22:01,637] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:22:01,637] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:22:01,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bf96188-3ca8-44ff-a591-52c13c7372ab/dqc_reference/checkm_data
[2023-03-15 10:22:01,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:22:01,644] [INFO] Task started: CheckM
[2023-03-15 10:22:01,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17565/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17565/checkm_input OceanDNA-b17565/checkm_result
[2023-03-15 10:22:33,661] [INFO] Task succeeded: CheckM
[2023-03-15 10:22:33,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:22:33,664] [INFO] ===== Completeness check finished =====
[2023-03-15 10:22:33,664] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:22:33,665] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17565/markers.fasta)
[2023-03-15 10:22:33,666] [INFO] Task started: Blastn
[2023-03-15 10:22:33,666] [INFO] Running command: blastn -query OceanDNA-b17565/markers.fasta -db /var/lib/cwl/stg1bf96188-3ca8-44ff-a591-52c13c7372ab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17565/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:22:34,644] [INFO] Task succeeded: Blastn
[2023-03-15 10:22:34,645] [INFO] Selected 24 target genomes.
[2023-03-15 10:22:34,645] [INFO] Target genome list was writen to OceanDNA-b17565/target_genomes_gtdb.txt
[2023-03-15 10:22:35,721] [INFO] Task started: fastANI
[2023-03-15 10:22:35,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c369c3f-8606-40c8-89ef-6771ba12ccea/OceanDNA-b17565.fa --refList OceanDNA-b17565/target_genomes_gtdb.txt --output OceanDNA-b17565/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:22:47,651] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:47,655] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:22:47,655] [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_009841265.1	s__JAAXHH01 sp009841265	76.6501	59	663	d__Bacteria;p__JAAXHH01;c__JAAXHH01;o__JAAXHH01;f__JAAXHH01;g__JAAXHH01	95.0	99.97	99.96	1.00	1.00	3	-
GCA_012270975.1	s__JAAXHH01 sp012270975	76.4881	76	663	d__Bacteria;p__JAAXHH01;c__JAAXHH01;o__JAAXHH01;f__JAAXHH01;g__JAAXHH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009835325.1	s__JAAXHH01 sp009835325	76.416	64	663	d__Bacteria;p__JAAXHH01;c__JAAXHH01;o__JAAXHH01;f__JAAXHH01;g__JAAXHH01	95.0	99.99	99.99	1.00	1.00	2	-
GCA_009837395.1	s__JAAXHH01 sp009837395	76.1426	78	663	d__Bacteria;p__JAAXHH01;c__JAAXHH01;o__JAAXHH01;f__JAAXHH01;g__JAAXHH01	95.0	98.47	97.89	0.97	0.94	5	-
GCA_009838645.1	s__JAAXHH01 sp009838645	76.0987	64	663	d__Bacteria;p__JAAXHH01;c__JAAXHH01;o__JAAXHH01;f__JAAXHH01;g__JAAXHH01	95.0	99.98	99.97	0.98	0.98	3	-
--------------------------------------------------------------------------------
[2023-03-15 10:22:47,655] [INFO] GTDB search result was written to OceanDNA-b17565/result_gtdb.tsv
[2023-03-15 10:22:47,656] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:22:47,656] [INFO] DFAST_QC result json was written to OceanDNA-b17565/dqc_result.json
[2023-03-15 10:22:47,657] [INFO] DFAST_QC completed!
[2023-03-15 10:22:47,657] [INFO] Total running time: 0h1m2s