[2023-03-15 15:51:29,967] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:51:29,967] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:51:29,967] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b4395ae-bcee-47e7-b78a-8135d56182de/dqc_reference
[2023-03-15 15:51:31,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:51:31,681] [INFO] Task started: Prodigal
[2023-03-15 15:51:31,681] [INFO] Running command: cat /var/lib/cwl/stg45245f65-2e25-47a3-837a-713e88e810d5/OceanDNA-b46760.fa | prodigal -d OceanDNA-b46760/cds.fna -a OceanDNA-b46760/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:51:53,972] [INFO] Task succeeded: Prodigal
[2023-03-15 15:51:53,972] [INFO] Task started: HMMsearch
[2023-03-15 15:51:53,972] [INFO] Running command: hmmsearch --tblout OceanDNA-b46760/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b4395ae-bcee-47e7-b78a-8135d56182de/dqc_reference/reference_markers.hmm OceanDNA-b46760/protein.faa > /dev/null
[2023-03-15 15:51:54,173] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:51:54,173] [INFO] Found 6/6 markers.
[2023-03-15 15:51:54,192] [INFO] Query marker FASTA was written to OceanDNA-b46760/markers.fasta
[2023-03-15 15:51:54,193] [INFO] Task started: Blastn
[2023-03-15 15:51:54,193] [INFO] Running command: blastn -query OceanDNA-b46760/markers.fasta -db /var/lib/cwl/stg0b4395ae-bcee-47e7-b78a-8135d56182de/dqc_reference/reference_markers.fasta -out OceanDNA-b46760/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:51:54,696] [INFO] Task succeeded: Blastn
[2023-03-15 15:51:54,697] [INFO] Selected 9 target genomes.
[2023-03-15 15:51:54,697] [INFO] Target genome list was writen to OceanDNA-b46760/target_genomes.txt
[2023-03-15 15:51:54,704] [INFO] Task started: fastANI
[2023-03-15 15:51:54,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg45245f65-2e25-47a3-837a-713e88e810d5/OceanDNA-b46760.fa --refList OceanDNA-b46760/target_genomes.txt --output OceanDNA-b46760/fastani_result.tsv --threads 1
[2023-03-15 15:52:02,007] [INFO] Task succeeded: fastANI
[2023-03-15 15:52:02,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b4395ae-bcee-47e7-b78a-8135d56182de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:52:02,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b4395ae-bcee-47e7-b78a-8135d56182de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:52:02,008] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:52:02,008] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:52:02,008] [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 15:52:02,008] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46760/tc_result.tsv
[2023-03-15 15:52:02,008] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:52:02,008] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:52:02,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b4395ae-bcee-47e7-b78a-8135d56182de/dqc_reference/checkm_data
[2023-03-15 15:52:02,011] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:52:02,016] [INFO] Task started: CheckM
[2023-03-15 15:52:02,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46760/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46760/checkm_input OceanDNA-b46760/checkm_result
[2023-03-15 15:52:59,787] [INFO] Task succeeded: CheckM
[2023-03-15 15:52:59,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.57%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 15:52:59,790] [INFO] ===== Completeness check finished =====
[2023-03-15 15:52:59,790] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:52:59,790] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46760/markers.fasta)
[2023-03-15 15:52:59,791] [INFO] Task started: Blastn
[2023-03-15 15:52:59,792] [INFO] Running command: blastn -query OceanDNA-b46760/markers.fasta -db /var/lib/cwl/stg0b4395ae-bcee-47e7-b78a-8135d56182de/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46760/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:53:00,519] [INFO] Task succeeded: Blastn
[2023-03-15 15:53:00,519] [INFO] Selected 10 target genomes.
[2023-03-15 15:53:00,519] [INFO] Target genome list was writen to OceanDNA-b46760/target_genomes_gtdb.txt
[2023-03-15 15:53:00,531] [INFO] Task started: fastANI
[2023-03-15 15:53:00,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg45245f65-2e25-47a3-837a-713e88e810d5/OceanDNA-b46760.fa --refList OceanDNA-b46760/target_genomes_gtdb.txt --output OceanDNA-b46760/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:53:08,434] [INFO] Task succeeded: fastANI
[2023-03-15 15:53:08,439] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:53:08,440] [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_002729275.1	s__Roseibacillus_B sp002729275	98.9306	823	900	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	98.94	98.88	0.91	0.89	3	conclusive
GCA_002420305.1	s__Roseibacillus_B sp002420305	83.8603	686	900	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	97.44	96.53	0.87	0.86	5	-
GCA_002380675.1	s__Roseibacillus_B sp002380675	83.1734	622	900	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.08	99.08	0.81	0.81	2	-
GCA_002686085.1	s__Roseibacillus_B sp002686085	82.8209	719	900	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.30	99.30	0.96	0.96	3	-
GCA_002709915.1	s__Roseibacillus_B sp002709915	80.5726	577	900	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.45	99.45	0.86	0.86	2	-
GCA_002715825.1	s__Roseibacillus_B sp002715825	80.4505	563	900	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.08	98.76	0.87	0.85	4	-
GCA_002723015.1	s__Roseibacillus_B sp002723015	78.7737	463	900	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.32	99.32	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-15 15:53:08,440] [INFO] GTDB search result was written to OceanDNA-b46760/result_gtdb.tsv
[2023-03-15 15:53:08,440] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:53:08,441] [INFO] DFAST_QC result json was written to OceanDNA-b46760/dqc_result.json
[2023-03-15 15:53:08,441] [INFO] DFAST_QC completed!
[2023-03-15 15:53:08,441] [INFO] Total running time: 0h1m38s