[2023-03-17 05:16:58,084] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:16:58,084] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:16:58,084] [INFO] DQC Reference Directory: /var/lib/cwl/stga173fabc-445f-42fc-a319-5d5dd88bd29c/dqc_reference
[2023-03-17 05:16:59,895] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:16:59,895] [INFO] Task started: Prodigal
[2023-03-17 05:16:59,896] [INFO] Running command: cat /var/lib/cwl/stg596d5707-fad7-4ed4-a6c6-f25af4d2703e/OceanDNA-b2139.fa | prodigal -d OceanDNA-b2139/cds.fna -a OceanDNA-b2139/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:17:03,313] [INFO] Task succeeded: Prodigal
[2023-03-17 05:17:03,313] [INFO] Task started: HMMsearch
[2023-03-17 05:17:03,314] [INFO] Running command: hmmsearch --tblout OceanDNA-b2139/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga173fabc-445f-42fc-a319-5d5dd88bd29c/dqc_reference/reference_markers.hmm OceanDNA-b2139/protein.faa > /dev/null
[2023-03-17 05:17:03,528] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:17:03,528] [INFO] Found 6/6 markers.
[2023-03-17 05:17:03,536] [INFO] Query marker FASTA was written to OceanDNA-b2139/markers.fasta
[2023-03-17 05:17:03,537] [INFO] Task started: Blastn
[2023-03-17 05:17:03,537] [INFO] Running command: blastn -query OceanDNA-b2139/markers.fasta -db /var/lib/cwl/stga173fabc-445f-42fc-a319-5d5dd88bd29c/dqc_reference/reference_markers.fasta -out OceanDNA-b2139/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:06,920] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:06,921] [INFO] Selected 16 target genomes.
[2023-03-17 05:17:06,921] [INFO] Target genome list was writen to OceanDNA-b2139/target_genomes.txt
[2023-03-17 05:17:07,205] [INFO] Task started: fastANI
[2023-03-17 05:17:07,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg596d5707-fad7-4ed4-a6c6-f25af4d2703e/OceanDNA-b2139.fa --refList OceanDNA-b2139/target_genomes.txt --output OceanDNA-b2139/fastani_result.tsv --threads 1
[2023-03-17 05:17:13,335] [INFO] Task succeeded: fastANI
[2023-03-17 05:17:13,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga173fabc-445f-42fc-a319-5d5dd88bd29c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:17:13,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga173fabc-445f-42fc-a319-5d5dd88bd29c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:17:13,336] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:17:13,336] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:17:13,336] [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 05:17:13,336] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2139/tc_result.tsv
[2023-03-17 05:17:13,336] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:17:13,336] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:17:13,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga173fabc-445f-42fc-a319-5d5dd88bd29c/dqc_reference/checkm_data
[2023-03-17 05:17:13,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:17:13,342] [INFO] Task started: CheckM
[2023-03-17 05:17:13,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2139/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2139/checkm_input OceanDNA-b2139/checkm_result
[2023-03-17 05:17:30,628] [INFO] Task succeeded: CheckM
[2023-03-17 05:17:30,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 5.68%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-03-17 05:17:30,630] [INFO] ===== Completeness check finished =====
[2023-03-17 05:17:30,630] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:17:30,630] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2139/markers.fasta)
[2023-03-17 05:17:30,632] [INFO] Task started: Blastn
[2023-03-17 05:17:30,632] [INFO] Running command: blastn -query OceanDNA-b2139/markers.fasta -db /var/lib/cwl/stga173fabc-445f-42fc-a319-5d5dd88bd29c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2139/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:32,224] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:32,224] [INFO] Selected 13 target genomes.
[2023-03-17 05:17:32,225] [INFO] Target genome list was writen to OceanDNA-b2139/target_genomes_gtdb.txt
[2023-03-17 05:17:32,281] [INFO] Task started: fastANI
[2023-03-17 05:17:32,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg596d5707-fad7-4ed4-a6c6-f25af4d2703e/OceanDNA-b2139.fa --refList OceanDNA-b2139/target_genomes_gtdb.txt --output OceanDNA-b2139/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:17:35,349] [INFO] Task succeeded: fastANI
[2023-03-17 05:17:35,354] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:17:35,355] [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_902533795.1	s__Actinomarina sp902533795	88.5962	180	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.75	95.75	0.81	0.81	2	-
GCA_902571385.1	s__Actinomarina sp902571385	88.3224	183	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.95	95.63	0.85	0.83	4	-
GCA_902604835.1	s__Actinomarina sp902604835	88.2327	165	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.34	95.34	0.81	0.81	2	-
GCA_902519845.1	s__Actinomarina sp902519845	88.1769	191	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.50	95.50	0.91	0.91	2	-
GCA_902609285.1	s__Actinomarina sp902609285	87.5405	160	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619825.1	s__Actinomarina sp902619825	80.8723	131	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.47	96.47	0.86	0.86	2	-
GCA_902627635.1	s__Actinomarina sp902627635	80.4476	105	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628045.1	s__Actinomarina sp902628045	76.8921	51	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:17:35,355] [INFO] GTDB search result was written to OceanDNA-b2139/result_gtdb.tsv
[2023-03-17 05:17:35,355] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:17:35,356] [INFO] DFAST_QC result json was written to OceanDNA-b2139/dqc_result.json
[2023-03-17 05:17:35,356] [INFO] DFAST_QC completed!
[2023-03-17 05:17:35,356] [INFO] Total running time: 0h0m37s