[2023-03-15 20:34:26,739] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,739] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,739] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd8317fc-f2cb-45e1-8020-4c98f5ece451/dqc_reference
[2023-03-15 20:34:28,460] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,460] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,460] [INFO] Running command: cat /var/lib/cwl/stgb85b1855-9977-4fc6-a4c6-a9fa734e6c9c/OceanDNA-b15520.fa | prodigal -d OceanDNA-b15520/cds.fna -a OceanDNA-b15520/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:46,420] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:46,421] [INFO] Task started: HMMsearch
[2023-03-15 20:34:46,421] [INFO] Running command: hmmsearch --tblout OceanDNA-b15520/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd8317fc-f2cb-45e1-8020-4c98f5ece451/dqc_reference/reference_markers.hmm OceanDNA-b15520/protein.faa > /dev/null
[2023-03-15 20:34:46,597] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:46,598] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb85b1855-9977-4fc6-a4c6-a9fa734e6c9c/OceanDNA-b15520.fa]
[2023-03-15 20:34:46,616] [INFO] Query marker FASTA was written to OceanDNA-b15520/markers.fasta
[2023-03-15 20:34:46,617] [INFO] Task started: Blastn
[2023-03-15 20:34:46,617] [INFO] Running command: blastn -query OceanDNA-b15520/markers.fasta -db /var/lib/cwl/stgfd8317fc-f2cb-45e1-8020-4c98f5ece451/dqc_reference/reference_markers.fasta -out OceanDNA-b15520/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:47,128] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:47,129] [INFO] Selected 13 target genomes.
[2023-03-15 20:34:47,129] [INFO] Target genome list was writen to OceanDNA-b15520/target_genomes.txt
[2023-03-15 20:34:47,136] [INFO] Task started: fastANI
[2023-03-15 20:34:47,136] [INFO] Running command: fastANI --query /var/lib/cwl/stgb85b1855-9977-4fc6-a4c6-a9fa734e6c9c/OceanDNA-b15520.fa --refList OceanDNA-b15520/target_genomes.txt --output OceanDNA-b15520/fastani_result.tsv --threads 1
[2023-03-15 20:34:55,068] [INFO] Task succeeded: fastANI
[2023-03-15 20:34:55,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd8317fc-f2cb-45e1-8020-4c98f5ece451/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:34:55,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd8317fc-f2cb-45e1-8020-4c98f5ece451/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:34:55,069] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:34:55,069] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 20:34:55,069] [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 20:34:55,069] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15520/tc_result.tsv
[2023-03-15 20:34:55,069] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:34:55,069] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:34:55,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd8317fc-f2cb-45e1-8020-4c98f5ece451/dqc_reference/checkm_data
[2023-03-15 20:34:55,072] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:34:55,076] [INFO] Task started: CheckM
[2023-03-15 20:34:55,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15520/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15520/checkm_input OceanDNA-b15520/checkm_result
[2023-03-15 20:35:41,062] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:41,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:35:41,531] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:41,531] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:41,531] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15520/markers.fasta)
[2023-03-15 20:35:41,531] [INFO] Task started: Blastn
[2023-03-15 20:35:41,531] [INFO] Running command: blastn -query OceanDNA-b15520/markers.fasta -db /var/lib/cwl/stgfd8317fc-f2cb-45e1-8020-4c98f5ece451/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15520/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:42,244] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:42,245] [INFO] Selected 16 target genomes.
[2023-03-15 20:35:42,245] [INFO] Target genome list was writen to OceanDNA-b15520/target_genomes_gtdb.txt
[2023-03-15 20:35:42,712] [INFO] Task started: fastANI
[2023-03-15 20:35:42,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgb85b1855-9977-4fc6-a4c6-a9fa734e6c9c/OceanDNA-b15520.fa --refList OceanDNA-b15520/target_genomes_gtdb.txt --output OceanDNA-b15520/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:50,238] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:50,243] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 20:35:50,243] [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_002311385.1	s__UBA1141 sp002311385	99.3275	914	963	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA1141	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002816455.1	s__UBA1141 sp002816455	78.5313	311	963	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA1141	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002817055.1	s__UBA1141 sp002817055	77.6523	171	963	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA1141	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746355.1	s__UBA9611 sp002746355	76.7318	99	963	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.11	98.97	0.93	0.85	6	-
GCA_013204585.1	s__UBA9611 sp013204585	76.6369	76	963	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392075.1	s__UBA9611 sp009392075	76.2634	56	963	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	96.71	96.71	0.58	0.58	2	-
GCA_009392095.1	s__UBA9611 sp009391975	76.1825	69	963	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.46	97.52	0.83	0.73	9	-
GCA_002698265.1	s__UBA9611 sp002698265	75.9338	55	963	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.74	98.13	0.78	0.72	6	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:50,243] [INFO] GTDB search result was written to OceanDNA-b15520/result_gtdb.tsv
[2023-03-15 20:35:50,244] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:50,244] [INFO] DFAST_QC result json was written to OceanDNA-b15520/dqc_result.json
[2023-03-15 20:35:50,244] [INFO] DFAST_QC completed!
[2023-03-15 20:35:50,244] [INFO] Total running time: 0h1m24s