[2023-03-15 13:54:30,582] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:54:30,582] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:54:30,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg653a72ce-36b0-4236-aed6-2550991cef49/dqc_reference
[2023-03-15 13:54:31,664] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:54:31,666] [INFO] Task started: Prodigal
[2023-03-15 13:54:31,666] [INFO] Running command: cat /var/lib/cwl/stg37ee7556-e7ad-4e47-8053-a6876f833245/OceanDNA-b10899.fa | prodigal -d OceanDNA-b10899/cds.fna -a OceanDNA-b10899/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:54:37,783] [INFO] Task succeeded: Prodigal
[2023-03-15 13:54:37,783] [INFO] Task started: HMMsearch
[2023-03-15 13:54:37,783] [INFO] Running command: hmmsearch --tblout OceanDNA-b10899/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg653a72ce-36b0-4236-aed6-2550991cef49/dqc_reference/reference_markers.hmm OceanDNA-b10899/protein.faa > /dev/null
[2023-03-15 13:54:37,911] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:54:37,912] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg37ee7556-e7ad-4e47-8053-a6876f833245/OceanDNA-b10899.fa]
[2023-03-15 13:54:37,942] [INFO] Query marker FASTA was written to OceanDNA-b10899/markers.fasta
[2023-03-15 13:54:37,943] [INFO] Task started: Blastn
[2023-03-15 13:54:37,943] [INFO] Running command: blastn -query OceanDNA-b10899/markers.fasta -db /var/lib/cwl/stg653a72ce-36b0-4236-aed6-2550991cef49/dqc_reference/reference_markers.fasta -out OceanDNA-b10899/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:54:38,438] [INFO] Task succeeded: Blastn
[2023-03-15 13:54:38,452] [INFO] Selected 13 target genomes.
[2023-03-15 13:54:38,452] [INFO] Target genome list was writen to OceanDNA-b10899/target_genomes.txt
[2023-03-15 13:54:38,460] [INFO] Task started: fastANI
[2023-03-15 13:54:38,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg37ee7556-e7ad-4e47-8053-a6876f833245/OceanDNA-b10899.fa --refList OceanDNA-b10899/target_genomes.txt --output OceanDNA-b10899/fastani_result.tsv --threads 1
[2023-03-15 13:54:44,425] [INFO] Task succeeded: fastANI
[2023-03-15 13:54:44,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg653a72ce-36b0-4236-aed6-2550991cef49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:54:44,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg653a72ce-36b0-4236-aed6-2550991cef49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:54:44,426] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:54:44,426] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:54:44,426] [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 13:54:44,429] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10899/tc_result.tsv
[2023-03-15 13:54:44,431] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:54:44,431] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:54:44,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg653a72ce-36b0-4236-aed6-2550991cef49/dqc_reference/checkm_data
[2023-03-15 13:54:44,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:54:44,453] [INFO] Task started: CheckM
[2023-03-15 13:54:44,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10899/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10899/checkm_input OceanDNA-b10899/checkm_result
[2023-03-15 13:55:05,889] [INFO] Task succeeded: CheckM
[2023-03-15 13:55:05,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:55:05,933] [INFO] ===== Completeness check finished =====
[2023-03-15 13:55:05,933] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:55:05,933] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10899/markers.fasta)
[2023-03-15 13:55:05,934] [INFO] Task started: Blastn
[2023-03-15 13:55:05,934] [INFO] Running command: blastn -query OceanDNA-b10899/markers.fasta -db /var/lib/cwl/stg653a72ce-36b0-4236-aed6-2550991cef49/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10899/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:55:06,523] [INFO] Task succeeded: Blastn
[2023-03-15 13:55:06,526] [INFO] Selected 7 target genomes.
[2023-03-15 13:55:06,526] [INFO] Target genome list was writen to OceanDNA-b10899/target_genomes_gtdb.txt
[2023-03-15 13:55:06,533] [INFO] Task started: fastANI
[2023-03-15 13:55:06,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg37ee7556-e7ad-4e47-8053-a6876f833245/OceanDNA-b10899.fa --refList OceanDNA-b10899/target_genomes_gtdb.txt --output OceanDNA-b10899/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:55:09,047] [INFO] Task succeeded: fastANI
[2023-03-15 13:55:09,053] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:55:09,053] [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_003023645.1	s__UBA7428 sp003023645	92.6079	218	234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.50	99.50	0.87	0.87	2	-
GCA_018608425.1	s__UBA7428 sp018608425	89.3408	174	234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477625.1	s__UBA7428 sp002477625	86.0943	182	234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.28	97.25	0.74	0.68	4	-
GCA_905181615.1	s__UBA7428 sp905181615	78.5086	136	234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
GCA_002708445.1	s__UBA7428 sp002708445	77.5314	66	234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:55:09,055] [INFO] GTDB search result was written to OceanDNA-b10899/result_gtdb.tsv
[2023-03-15 13:55:09,055] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:55:09,058] [INFO] DFAST_QC result json was written to OceanDNA-b10899/dqc_result.json
[2023-03-15 13:55:09,058] [INFO] DFAST_QC completed!
[2023-03-15 13:55:09,058] [INFO] Total running time: 0h0m38s