[2023-03-16 05:27:23,951] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:27:23,960] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:27:23,960] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc178cce-f01c-4f95-9709-10afec3468d8/dqc_reference
[2023-03-16 05:27:25,056] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:27:25,057] [INFO] Task started: Prodigal
[2023-03-16 05:27:25,057] [INFO] Running command: cat /var/lib/cwl/stg1ff928d2-e29d-49fb-9d84-9dae20294c4f/OceanDNA-b3298.fa | prodigal -d OceanDNA-b3298/cds.fna -a OceanDNA-b3298/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:27:32,873] [INFO] Task succeeded: Prodigal
[2023-03-16 05:27:32,873] [INFO] Task started: HMMsearch
[2023-03-16 05:27:32,873] [INFO] Running command: hmmsearch --tblout OceanDNA-b3298/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc178cce-f01c-4f95-9709-10afec3468d8/dqc_reference/reference_markers.hmm OceanDNA-b3298/protein.faa > /dev/null
[2023-03-16 05:27:33,060] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:27:33,060] [INFO] Found 6/6 markers.
[2023-03-16 05:27:33,157] [INFO] Query marker FASTA was written to OceanDNA-b3298/markers.fasta
[2023-03-16 05:27:33,157] [INFO] Task started: Blastn
[2023-03-16 05:27:33,157] [INFO] Running command: blastn -query OceanDNA-b3298/markers.fasta -db /var/lib/cwl/stgdc178cce-f01c-4f95-9709-10afec3468d8/dqc_reference/reference_markers.fasta -out OceanDNA-b3298/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:27:33,678] [INFO] Task succeeded: Blastn
[2023-03-16 05:27:33,700] [INFO] Selected 20 target genomes.
[2023-03-16 05:27:33,700] [INFO] Target genome list was writen to OceanDNA-b3298/target_genomes.txt
[2023-03-16 05:27:33,710] [INFO] Task started: fastANI
[2023-03-16 05:27:33,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ff928d2-e29d-49fb-9d84-9dae20294c4f/OceanDNA-b3298.fa --refList OceanDNA-b3298/target_genomes.txt --output OceanDNA-b3298/fastani_result.tsv --threads 1
[2023-03-16 05:27:44,665] [INFO] Task succeeded: fastANI
[2023-03-16 05:27:44,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc178cce-f01c-4f95-9709-10afec3468d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:27:44,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc178cce-f01c-4f95-9709-10afec3468d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:27:44,666] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:27:44,666] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:27:44,666] [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
--------------------------------------------------------------------------------
[2023-03-16 05:27:44,675] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3298/tc_result.tsv
[2023-03-16 05:27:44,697] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:27:44,697] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:27:44,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc178cce-f01c-4f95-9709-10afec3468d8/dqc_reference/checkm_data
[2023-03-16 05:27:44,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:27:44,724] [INFO] Task started: CheckM
[2023-03-16 05:27:44,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3298/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3298/checkm_input OceanDNA-b3298/checkm_result
[2023-03-16 05:28:09,529] [INFO] Task succeeded: CheckM
[2023-03-16 05:28:09,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:28:09,627] [INFO] ===== Completeness check finished =====
[2023-03-16 05:28:09,627] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:28:09,627] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3298/markers.fasta)
[2023-03-16 05:28:09,628] [INFO] Task started: Blastn
[2023-03-16 05:28:09,628] [INFO] Running command: blastn -query OceanDNA-b3298/markers.fasta -db /var/lib/cwl/stgdc178cce-f01c-4f95-9709-10afec3468d8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3298/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:28:10,296] [INFO] Task succeeded: Blastn
[2023-03-16 05:28:10,297] [INFO] Selected 14 target genomes.
[2023-03-16 05:28:10,297] [INFO] Target genome list was writen to OceanDNA-b3298/target_genomes_gtdb.txt
[2023-03-16 05:28:10,309] [INFO] Task started: fastANI
[2023-03-16 05:28:10,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ff928d2-e29d-49fb-9d84-9dae20294c4f/OceanDNA-b3298.fa --refList OceanDNA-b3298/target_genomes_gtdb.txt --output OceanDNA-b3298/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:28:13,654] [INFO] Task succeeded: fastANI
[2023-03-16 05:28:13,659] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:28:13,659] [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_002430405.1	s__UBA5976 sp002430405	99.4051	322	428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009702945.1	s__UBA5976 sp009702945	79.3364	109	428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009698575.1	s__UBA5976 sp009698575	79.0603	172	428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	99.89	99.66	0.97	0.94	7	-
GCA_009918005.1	s__UBA5976 sp009918005	79.0513	134	428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903925705.1	s__UBA5976 sp903925705	78.2616	113	428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903951185.1	s__UBA5976 sp903951185	76.572	51	428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	99.15	99.15	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-16 05:28:13,659] [INFO] GTDB search result was written to OceanDNA-b3298/result_gtdb.tsv
[2023-03-16 05:28:13,659] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:28:13,660] [INFO] DFAST_QC result json was written to OceanDNA-b3298/dqc_result.json
[2023-03-16 05:28:13,660] [INFO] DFAST_QC completed!
[2023-03-16 05:28:13,660] [INFO] Total running time: 0h0m50s