[2023-03-14 13:28:14,711] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:28:14,711] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:28:14,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg429c098c-60de-4cbe-9646-71db8ce7ca42/dqc_reference
[2023-03-14 13:28:15,816] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:28:15,816] [INFO] Task started: Prodigal
[2023-03-14 13:28:15,816] [INFO] Running command: cat /var/lib/cwl/stg83896269-4612-41e9-adc6-383d65b69b25/OceanDNA-b2050.fa | prodigal -d OceanDNA-b2050/cds.fna -a OceanDNA-b2050/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:28:19,824] [INFO] Task succeeded: Prodigal
[2023-03-14 13:28:19,824] [INFO] Task started: HMMsearch
[2023-03-14 13:28:19,824] [INFO] Running command: hmmsearch --tblout OceanDNA-b2050/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg429c098c-60de-4cbe-9646-71db8ce7ca42/dqc_reference/reference_markers.hmm OceanDNA-b2050/protein.faa > /dev/null
[2023-03-14 13:28:19,979] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:28:19,979] [INFO] Found 6/6 markers.
[2023-03-14 13:28:20,386] [INFO] Query marker FASTA was written to OceanDNA-b2050/markers.fasta
[2023-03-14 13:28:20,386] [INFO] Task started: Blastn
[2023-03-14 13:28:20,387] [INFO] Running command: blastn -query OceanDNA-b2050/markers.fasta -db /var/lib/cwl/stg429c098c-60de-4cbe-9646-71db8ce7ca42/dqc_reference/reference_markers.fasta -out OceanDNA-b2050/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:28:20,930] [INFO] Task succeeded: Blastn
[2023-03-14 13:28:20,931] [INFO] Selected 13 target genomes.
[2023-03-14 13:28:20,931] [INFO] Target genome list was writen to OceanDNA-b2050/target_genomes.txt
[2023-03-14 13:28:20,938] [INFO] Task started: fastANI
[2023-03-14 13:28:20,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg83896269-4612-41e9-adc6-383d65b69b25/OceanDNA-b2050.fa --refList OceanDNA-b2050/target_genomes.txt --output OceanDNA-b2050/fastani_result.tsv --threads 1
[2023-03-14 13:28:26,485] [INFO] Task succeeded: fastANI
[2023-03-14 13:28:26,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg429c098c-60de-4cbe-9646-71db8ce7ca42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:28:26,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg429c098c-60de-4cbe-9646-71db8ce7ca42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:28:26,486] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:28:26,486] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:28:26,486] [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
--------------------------------------------------------------------------------
[2023-03-14 13:28:26,486] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2050/tc_result.tsv
[2023-03-14 13:28:26,486] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:28:26,486] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:28:26,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg429c098c-60de-4cbe-9646-71db8ce7ca42/dqc_reference/checkm_data
[2023-03-14 13:28:26,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:28:26,491] [INFO] Task started: CheckM
[2023-03-14 13:28:26,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2050/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2050/checkm_input OceanDNA-b2050/checkm_result
[2023-03-14 13:28:42,619] [INFO] Task succeeded: CheckM
[2023-03-14 13:28:42,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:28:42,620] [INFO] ===== Completeness check finished =====
[2023-03-14 13:28:42,621] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:28:42,621] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2050/markers.fasta)
[2023-03-14 13:28:42,622] [INFO] Task started: Blastn
[2023-03-14 13:28:42,622] [INFO] Running command: blastn -query OceanDNA-b2050/markers.fasta -db /var/lib/cwl/stg429c098c-60de-4cbe-9646-71db8ce7ca42/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2050/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:28:43,325] [INFO] Task succeeded: Blastn
[2023-03-14 13:28:43,326] [INFO] Selected 16 target genomes.
[2023-03-14 13:28:43,326] [INFO] Target genome list was writen to OceanDNA-b2050/target_genomes_gtdb.txt
[2023-03-14 13:28:43,342] [INFO] Task started: fastANI
[2023-03-14 13:28:43,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg83896269-4612-41e9-adc6-383d65b69b25/OceanDNA-b2050.fa --refList OceanDNA-b2050/target_genomes_gtdb.txt --output OceanDNA-b2050/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:28:45,876] [INFO] Task succeeded: fastANI
[2023-03-14 13:28:45,883] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:28:45,883] [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_014384285.1	s__Actinomarina sp014384285	98.5257	247	260	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	99.05	98.78	0.90	0.82	4	conclusive
GCA_002308095.1	s__Actinomarina sp002308095	81.1199	125	260	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239265.1	s__Actinomarina sp014239265	80.066	152	260	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510965.1	s__Actinomarina sp002683085	79.9206	124	260	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.49	98.44	0.76	0.76	3	-
GCA_002169845.1	s__Actinomarina sp002169845	79.668	89	260	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002169115.2	s__Actinomarina sp002169115	78.2193	53	260	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.47	96.47	0.52	0.52	2	-
GCA_003282445.1	s__Actinomarina sp003282445	77.6579	61	260	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.01	96.02	0.90	0.85	11	-
GCA_902595195.1	s__Actinomarina sp902595195	77.326	53	260	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.26	97.26	0.73	0.73	2	-
GCA_902580215.1	s__Actinomarina sp902580215	77.2406	50	260	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.48	95.05	0.79	0.77	5	-
GCA_902510995.1	s__Actinomarina sp902510995	76.9634	60	260	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.36	95.36	0.76	0.76	2	-
GCA_902596545.1	s__Actinomarina sp902596545	76.6516	59	260	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.42	98.42	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-14 13:28:45,883] [INFO] GTDB search result was written to OceanDNA-b2050/result_gtdb.tsv
[2023-03-14 13:28:45,883] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:28:45,884] [INFO] DFAST_QC result json was written to OceanDNA-b2050/dqc_result.json
[2023-03-14 13:28:45,884] [INFO] DFAST_QC completed!
[2023-03-14 13:28:45,884] [INFO] Total running time: 0h0m31s