[2023-03-15 11:51:17,348] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:51:17,348] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:51:17,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg071fbba3-10ce-4d3c-9cc9-da43f1f3f9be/dqc_reference
[2023-03-15 11:51:18,950] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:51:18,951] [INFO] Task started: Prodigal
[2023-03-15 11:51:18,951] [INFO] Running command: cat /var/lib/cwl/stg7a77eaff-c311-485d-9ea4-feca092fd82d/OceanDNA-b11025.fa | prodigal -d OceanDNA-b11025/cds.fna -a OceanDNA-b11025/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:51:30,497] [INFO] Task succeeded: Prodigal
[2023-03-15 11:51:30,497] [INFO] Task started: HMMsearch
[2023-03-15 11:51:30,497] [INFO] Running command: hmmsearch --tblout OceanDNA-b11025/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg071fbba3-10ce-4d3c-9cc9-da43f1f3f9be/dqc_reference/reference_markers.hmm OceanDNA-b11025/protein.faa > /dev/null
[2023-03-15 11:51:30,668] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:51:30,669] [INFO] Found 6/6 markers.
[2023-03-15 11:51:30,682] [INFO] Query marker FASTA was written to OceanDNA-b11025/markers.fasta
[2023-03-15 11:51:30,682] [INFO] Task started: Blastn
[2023-03-15 11:51:30,682] [INFO] Running command: blastn -query OceanDNA-b11025/markers.fasta -db /var/lib/cwl/stg071fbba3-10ce-4d3c-9cc9-da43f1f3f9be/dqc_reference/reference_markers.fasta -out OceanDNA-b11025/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:51:31,266] [INFO] Task succeeded: Blastn
[2023-03-15 11:51:31,267] [INFO] Selected 34 target genomes.
[2023-03-15 11:51:31,267] [INFO] Target genome list was writen to OceanDNA-b11025/target_genomes.txt
[2023-03-15 11:51:31,289] [INFO] Task started: fastANI
[2023-03-15 11:51:31,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a77eaff-c311-485d-9ea4-feca092fd82d/OceanDNA-b11025.fa --refList OceanDNA-b11025/target_genomes.txt --output OceanDNA-b11025/fastani_result.tsv --threads 1
[2023-03-15 11:51:48,623] [INFO] Task succeeded: fastANI
[2023-03-15 11:51:48,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg071fbba3-10ce-4d3c-9cc9-da43f1f3f9be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:51:48,624] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg071fbba3-10ce-4d3c-9cc9-da43f1f3f9be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:51:48,624] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:51:48,624] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:51:48,624] [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 11:51:48,624] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11025/tc_result.tsv
[2023-03-15 11:51:48,624] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:51:48,624] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:51:48,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg071fbba3-10ce-4d3c-9cc9-da43f1f3f9be/dqc_reference/checkm_data
[2023-03-15 11:51:48,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:51:48,631] [INFO] Task started: CheckM
[2023-03-15 11:51:48,631] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11025/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11025/checkm_input OceanDNA-b11025/checkm_result
[2023-03-15 11:52:22,001] [INFO] Task succeeded: CheckM
[2023-03-15 11:52:22,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:52:22,003] [INFO] ===== Completeness check finished =====
[2023-03-15 11:52:22,003] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:52:22,004] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11025/markers.fasta)
[2023-03-15 11:52:22,004] [INFO] Task started: Blastn
[2023-03-15 11:52:22,004] [INFO] Running command: blastn -query OceanDNA-b11025/markers.fasta -db /var/lib/cwl/stg071fbba3-10ce-4d3c-9cc9-da43f1f3f9be/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11025/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:52:22,801] [INFO] Task succeeded: Blastn
[2023-03-15 11:52:22,802] [INFO] Selected 13 target genomes.
[2023-03-15 11:52:22,802] [INFO] Target genome list was writen to OceanDNA-b11025/target_genomes_gtdb.txt
[2023-03-15 11:52:22,816] [INFO] Task started: fastANI
[2023-03-15 11:52:22,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a77eaff-c311-485d-9ea4-feca092fd82d/OceanDNA-b11025.fa --refList OceanDNA-b11025/target_genomes_gtdb.txt --output OceanDNA-b11025/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:52:28,700] [INFO] Task succeeded: fastANI
[2023-03-15 11:52:28,705] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:52:28,706] [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	96.1155	444	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.50	99.50	0.87	0.87	2	conclusive
GCA_018608425.1	s__UBA7428 sp018608425	90.8721	354	544	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	87.4539	363	544	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	79.3193	286	544	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	77.8082	157	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182575.1	s__UBA8316 sp905182575	77.1693	62	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	95.72	95.72	0.87	0.87	2	-
GCA_009886625.1	s__MS024-2A sp009886625	76.3244	52	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:52:28,706] [INFO] GTDB search result was written to OceanDNA-b11025/result_gtdb.tsv
[2023-03-15 11:52:28,706] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:52:28,707] [INFO] DFAST_QC result json was written to OceanDNA-b11025/dqc_result.json
[2023-03-15 11:52:28,707] [INFO] DFAST_QC completed!
[2023-03-15 11:52:28,707] [INFO] Total running time: 0h1m11s