[2023-03-15 23:56:02,718] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:56:02,720] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:56:02,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f39f0dc-2d2c-4fed-8392-e6bdff629d2c/dqc_reference
[2023-03-15 23:56:03,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:56:03,850] [INFO] Task started: Prodigal
[2023-03-15 23:56:03,851] [INFO] Running command: cat /var/lib/cwl/stg9e7fcf49-fe77-4e30-a295-756b7b2b0778/OceanDNA-b46725.fa | prodigal -d OceanDNA-b46725/cds.fna -a OceanDNA-b46725/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:56:25,521] [INFO] Task succeeded: Prodigal
[2023-03-15 23:56:25,521] [INFO] Task started: HMMsearch
[2023-03-15 23:56:25,522] [INFO] Running command: hmmsearch --tblout OceanDNA-b46725/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f39f0dc-2d2c-4fed-8392-e6bdff629d2c/dqc_reference/reference_markers.hmm OceanDNA-b46725/protein.faa > /dev/null
[2023-03-15 23:56:25,731] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:56:25,731] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9e7fcf49-fe77-4e30-a295-756b7b2b0778/OceanDNA-b46725.fa]
[2023-03-15 23:56:25,763] [INFO] Query marker FASTA was written to OceanDNA-b46725/markers.fasta
[2023-03-15 23:56:25,764] [INFO] Task started: Blastn
[2023-03-15 23:56:25,765] [INFO] Running command: blastn -query OceanDNA-b46725/markers.fasta -db /var/lib/cwl/stg9f39f0dc-2d2c-4fed-8392-e6bdff629d2c/dqc_reference/reference_markers.fasta -out OceanDNA-b46725/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:56:26,269] [INFO] Task succeeded: Blastn
[2023-03-15 23:56:26,275] [INFO] Selected 16 target genomes.
[2023-03-15 23:56:26,275] [INFO] Target genome list was writen to OceanDNA-b46725/target_genomes.txt
[2023-03-15 23:56:26,287] [INFO] Task started: fastANI
[2023-03-15 23:56:26,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e7fcf49-fe77-4e30-a295-756b7b2b0778/OceanDNA-b46725.fa --refList OceanDNA-b46725/target_genomes.txt --output OceanDNA-b46725/fastani_result.tsv --threads 1
[2023-03-15 23:56:37,085] [INFO] Task succeeded: fastANI
[2023-03-15 23:56:37,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f39f0dc-2d2c-4fed-8392-e6bdff629d2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:56:37,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f39f0dc-2d2c-4fed-8392-e6bdff629d2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:56:37,086] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:56:37,086] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:56:37,086] [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 23:56:37,091] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46725/tc_result.tsv
[2023-03-15 23:56:37,099] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:56:37,099] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:56:37,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f39f0dc-2d2c-4fed-8392-e6bdff629d2c/dqc_reference/checkm_data
[2023-03-15 23:56:37,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:56:37,117] [INFO] Task started: CheckM
[2023-03-15 23:56:37,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46725/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46725/checkm_input OceanDNA-b46725/checkm_result
[2023-03-15 23:57:34,453] [INFO] Task succeeded: CheckM
[2023-03-15 23:57:34,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.10%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:57:34,522] [INFO] ===== Completeness check finished =====
[2023-03-15 23:57:34,522] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:57:34,522] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46725/markers.fasta)
[2023-03-15 23:57:34,524] [INFO] Task started: Blastn
[2023-03-15 23:57:34,524] [INFO] Running command: blastn -query OceanDNA-b46725/markers.fasta -db /var/lib/cwl/stg9f39f0dc-2d2c-4fed-8392-e6bdff629d2c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46725/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:57:35,166] [INFO] Task succeeded: Blastn
[2023-03-15 23:57:35,171] [INFO] Selected 14 target genomes.
[2023-03-15 23:57:35,171] [INFO] Target genome list was writen to OceanDNA-b46725/target_genomes_gtdb.txt
[2023-03-15 23:57:35,249] [INFO] Task started: fastANI
[2023-03-15 23:57:35,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e7fcf49-fe77-4e30-a295-756b7b2b0778/OceanDNA-b46725.fa --refList OceanDNA-b46725/target_genomes_gtdb.txt --output OceanDNA-b46725/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:57:43,376] [INFO] Task succeeded: fastANI
[2023-03-15 23:57:43,383] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:57:43,383] [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_002709395.1	s__Roseibacillus_B sp002709395	97.2241	554	651	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	97.31	97.31	0.76	0.76	2	conclusive
GCA_002501065.1	s__Roseibacillus_B sp002501065	78.3949	318	651	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.61	99.55	0.90	0.89	3	-
GCA_002721695.1	s__Roseibacillus_B sp002721695	78.3467	180	651	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240355.1	s__Roseibacillus_B sp014240355	78.339	247	651	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483645.1	s__Roseibacillus_B sp003483645	77.8278	198	651	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002420305.1	s__Roseibacillus_B sp002420305	77.7834	149	651	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_002686085.1	s__Roseibacillus_B sp002686085	77.5446	166	651	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_002729275.1	s__Roseibacillus_B sp002729275	77.4205	116	651	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	98.94	98.88	0.91	0.89	3	-
GCA_002715825.1	s__Roseibacillus_B sp002715825	77.3285	135	651	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	77.2222	152	651	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 23:57:43,384] [INFO] GTDB search result was written to OceanDNA-b46725/result_gtdb.tsv
[2023-03-15 23:57:43,384] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:57:43,386] [INFO] DFAST_QC result json was written to OceanDNA-b46725/dqc_result.json
[2023-03-15 23:57:43,387] [INFO] DFAST_QC completed!
[2023-03-15 23:57:43,387] [INFO] Total running time: 0h1m41s