[2023-03-15 23:42:29,666] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:42:29,667] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:42:29,667] [INFO] DQC Reference Directory: /var/lib/cwl/stg857e77f3-358c-4344-9510-82042521b14c/dqc_reference
[2023-03-15 23:42:31,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:42:31,275] [INFO] Task started: Prodigal
[2023-03-15 23:42:31,275] [INFO] Running command: cat /var/lib/cwl/stg2aecaeee-82f7-4b5a-836f-7367c40fa52e/OceanDNA-b47092.fa | prodigal -d OceanDNA-b47092/cds.fna -a OceanDNA-b47092/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:42:59,389] [INFO] Task succeeded: Prodigal
[2023-03-15 23:42:59,389] [INFO] Task started: HMMsearch
[2023-03-15 23:42:59,389] [INFO] Running command: hmmsearch --tblout OceanDNA-b47092/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg857e77f3-358c-4344-9510-82042521b14c/dqc_reference/reference_markers.hmm OceanDNA-b47092/protein.faa > /dev/null
[2023-03-15 23:42:59,608] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:42:59,609] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2aecaeee-82f7-4b5a-836f-7367c40fa52e/OceanDNA-b47092.fa]
[2023-03-15 23:42:59,638] [INFO] Query marker FASTA was written to OceanDNA-b47092/markers.fasta
[2023-03-15 23:42:59,639] [INFO] Task started: Blastn
[2023-03-15 23:42:59,639] [INFO] Running command: blastn -query OceanDNA-b47092/markers.fasta -db /var/lib/cwl/stg857e77f3-358c-4344-9510-82042521b14c/dqc_reference/reference_markers.fasta -out OceanDNA-b47092/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:43:00,151] [INFO] Task succeeded: Blastn
[2023-03-15 23:43:00,151] [INFO] Selected 14 target genomes.
[2023-03-15 23:43:00,152] [INFO] Target genome list was writen to OceanDNA-b47092/target_genomes.txt
[2023-03-15 23:43:00,161] [INFO] Task started: fastANI
[2023-03-15 23:43:00,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aecaeee-82f7-4b5a-836f-7367c40fa52e/OceanDNA-b47092.fa --refList OceanDNA-b47092/target_genomes.txt --output OceanDNA-b47092/fastani_result.tsv --threads 1
[2023-03-15 23:43:11,860] [INFO] Task succeeded: fastANI
[2023-03-15 23:43:11,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg857e77f3-358c-4344-9510-82042521b14c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:43:11,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg857e77f3-358c-4344-9510-82042521b14c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:43:11,865] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:43:11,865] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:43:11,865] [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
Prosthecobacter dejongeii	strain=DSM 12251	GCA_014203045.1	48465	48465	type	True	78.5077	306	726	95	below_threshold
Prosthecobacter fusiformis	strain=ATCC 25309	GCA_004364345.1	48464	48464	type	True	78.3538	261	726	95	below_threshold
Prosthecobacter debontii	strain=ATCC 700200	GCA_900167535.1	48467	48467	type	True	78.1418	236	726	95	below_threshold
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	76.8943	81	726	95	below_threshold
Brevifollis gellanilyticus	strain=NBRC 108608	GCA_007992435.1	748831	748831	type	True	76.6445	120	726	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:43:11,866] [INFO] DFAST Taxonomy check result was written to OceanDNA-b47092/tc_result.tsv
[2023-03-15 23:43:11,866] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:43:11,866] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:43:11,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg857e77f3-358c-4344-9510-82042521b14c/dqc_reference/checkm_data
[2023-03-15 23:43:11,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:43:11,905] [INFO] Task started: CheckM
[2023-03-15 23:43:11,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b47092/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b47092/checkm_input OceanDNA-b47092/checkm_result
[2023-03-15 23:44:25,901] [INFO] Task succeeded: CheckM
[2023-03-15 23:44:25,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.41%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:44:25,905] [INFO] ===== Completeness check finished =====
[2023-03-15 23:44:25,905] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:44:25,905] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b47092/markers.fasta)
[2023-03-15 23:44:25,906] [INFO] Task started: Blastn
[2023-03-15 23:44:25,906] [INFO] Running command: blastn -query OceanDNA-b47092/markers.fasta -db /var/lib/cwl/stg857e77f3-358c-4344-9510-82042521b14c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b47092/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:44:26,641] [INFO] Task succeeded: Blastn
[2023-03-15 23:44:26,643] [INFO] Selected 16 target genomes.
[2023-03-15 23:44:26,643] [INFO] Target genome list was writen to OceanDNA-b47092/target_genomes_gtdb.txt
[2023-03-15 23:44:26,695] [INFO] Task started: fastANI
[2023-03-15 23:44:26,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aecaeee-82f7-4b5a-836f-7367c40fa52e/OceanDNA-b47092.fa --refList OceanDNA-b47092/target_genomes_gtdb.txt --output OceanDNA-b47092/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:44:40,901] [INFO] Task succeeded: fastANI
[2023-03-15 23:44:40,908] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:44:40,908] [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
GCF_014203045.1	s__Prosthecobacter dejongeii	78.4943	307	726	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003453085.1	s__Prosthecobacter sp003453085	78.3927	170	726	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364345.1	s__Prosthecobacter fusiformis	78.3674	260	726	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167535.1	s__Prosthecobacter debontii	78.1578	235	726	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203095.1	s__Prosthecobacter vanneervenii	76.9224	80	726	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017301975.1	s__Prosthecobacter sp017301975	76.898	79	726	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903960845.1	s__Prosthecobacter sp903960845	76.6862	97	726	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	99.18	98.90	0.84	0.82	4	-
GCF_007992435.1	s__Prosthecobacter gellanilyticus	76.6582	118	726	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482965.1	s__Prosthecobacter sp002482965	76.6336	87	726	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336895.1	s__Prosthecobacter sp002336895	76.5874	93	726	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:44:40,909] [INFO] GTDB search result was written to OceanDNA-b47092/result_gtdb.tsv
[2023-03-15 23:44:40,909] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:44:40,910] [INFO] DFAST_QC result json was written to OceanDNA-b47092/dqc_result.json
[2023-03-15 23:44:40,910] [INFO] DFAST_QC completed!
[2023-03-15 23:44:40,910] [INFO] Total running time: 0h2m11s