[2023-03-17 05:39:41,242] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:39:41,242] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:39:41,242] [INFO] DQC Reference Directory: /var/lib/cwl/stgda441a04-f8dc-4066-96a5-c1ffb8b65cc9/dqc_reference
[2023-03-17 05:39:42,411] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:39:42,411] [INFO] Task started: Prodigal
[2023-03-17 05:39:42,411] [INFO] Running command: cat /var/lib/cwl/stgdedb3262-b870-4768-9d1c-7985b9efd21a/OceanDNA-b2034.fa | prodigal -d OceanDNA-b2034/cds.fna -a OceanDNA-b2034/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:39:46,561] [INFO] Task succeeded: Prodigal
[2023-03-17 05:39:46,562] [INFO] Task started: HMMsearch
[2023-03-17 05:39:46,562] [INFO] Running command: hmmsearch --tblout OceanDNA-b2034/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda441a04-f8dc-4066-96a5-c1ffb8b65cc9/dqc_reference/reference_markers.hmm OceanDNA-b2034/protein.faa > /dev/null
[2023-03-17 05:39:46,715] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:39:46,715] [INFO] Found 6/6 markers.
[2023-03-17 05:39:46,723] [INFO] Query marker FASTA was written to OceanDNA-b2034/markers.fasta
[2023-03-17 05:39:46,723] [INFO] Task started: Blastn
[2023-03-17 05:39:46,723] [INFO] Running command: blastn -query OceanDNA-b2034/markers.fasta -db /var/lib/cwl/stgda441a04-f8dc-4066-96a5-c1ffb8b65cc9/dqc_reference/reference_markers.fasta -out OceanDNA-b2034/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:39:47,225] [INFO] Task succeeded: Blastn
[2023-03-17 05:39:47,225] [INFO] Selected 12 target genomes.
[2023-03-17 05:39:47,225] [INFO] Target genome list was writen to OceanDNA-b2034/target_genomes.txt
[2023-03-17 05:39:47,233] [INFO] Task started: fastANI
[2023-03-17 05:39:47,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgdedb3262-b870-4768-9d1c-7985b9efd21a/OceanDNA-b2034.fa --refList OceanDNA-b2034/target_genomes.txt --output OceanDNA-b2034/fastani_result.tsv --threads 1
[2023-03-17 05:39:53,264] [INFO] Task succeeded: fastANI
[2023-03-17 05:39:53,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda441a04-f8dc-4066-96a5-c1ffb8b65cc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:39:53,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda441a04-f8dc-4066-96a5-c1ffb8b65cc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:39:53,265] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:39:53,265] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:39:53,265] [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
--------------------------------------------------------------------------------
[2023-03-17 05:39:53,265] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2034/tc_result.tsv
[2023-03-17 05:39:53,265] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:39:53,265] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:39:53,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda441a04-f8dc-4066-96a5-c1ffb8b65cc9/dqc_reference/checkm_data
[2023-03-17 05:39:53,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:39:53,270] [INFO] Task started: CheckM
[2023-03-17 05:39:53,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2034/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2034/checkm_input OceanDNA-b2034/checkm_result
[2023-03-17 05:40:10,500] [INFO] Task succeeded: CheckM
[2023-03-17 05:40:10,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:40:10,505] [INFO] ===== Completeness check finished =====
[2023-03-17 05:40:10,505] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:40:10,505] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2034/markers.fasta)
[2023-03-17 05:40:10,505] [INFO] Task started: Blastn
[2023-03-17 05:40:10,505] [INFO] Running command: blastn -query OceanDNA-b2034/markers.fasta -db /var/lib/cwl/stgda441a04-f8dc-4066-96a5-c1ffb8b65cc9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2034/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:40:11,613] [INFO] Task succeeded: Blastn
[2023-03-17 05:40:11,614] [INFO] Selected 15 target genomes.
[2023-03-17 05:40:11,614] [INFO] Target genome list was writen to OceanDNA-b2034/target_genomes_gtdb.txt
[2023-03-17 05:40:11,706] [INFO] Task started: fastANI
[2023-03-17 05:40:11,707] [INFO] Running command: fastANI --query /var/lib/cwl/stgdedb3262-b870-4768-9d1c-7985b9efd21a/OceanDNA-b2034.fa --refList OceanDNA-b2034/target_genomes_gtdb.txt --output OceanDNA-b2034/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:40:15,617] [INFO] Task succeeded: fastANI
[2023-03-17 05:40:15,623] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:40:15,623] [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_902565645.1	s__Actinomarina sp902565645	97.8565	211	277	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902510995.1	s__Actinomarina sp902510995	81.3327	173	277	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.36	95.36	0.76	0.76	2	-
GCA_004214055.1	s__Actinomarina sp004214055	81.1433	132	277	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282445.1	s__Actinomarina sp003282445	81.1357	202	277	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.01	96.02	0.90	0.85	11	-
GCA_002724835.1	s__Actinomarina sp002724835	80.9931	165	277	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.97	95.84	0.72	0.71	4	-
GCA_902533795.1	s__Actinomarina sp902533795	76.89	68	277	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.75	95.75	0.81	0.81	2	-
GCA_902593795.1	s__Actinomarina sp902593795	76.8724	66	277	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.69	97.47	0.86	0.85	3	-
GCA_902627635.1	s__Actinomarina sp902627635	76.7901	66	277	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626065.1	s__Actinomarina sp902626065	76.7839	75	277	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.15	96.15	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-17 05:40:15,623] [INFO] GTDB search result was written to OceanDNA-b2034/result_gtdb.tsv
[2023-03-17 05:40:15,623] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:40:15,624] [INFO] DFAST_QC result json was written to OceanDNA-b2034/dqc_result.json
[2023-03-17 05:40:15,624] [INFO] DFAST_QC completed!
[2023-03-17 05:40:15,624] [INFO] Total running time: 0h0m34s