[2023-03-14 12:13:42,663] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:13:42,664] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:13:42,664] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c8eb785-69b9-48f0-888b-a37db6c62b96/dqc_reference
[2023-03-14 12:13:44,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:13:44,621] [INFO] Task started: Prodigal
[2023-03-14 12:13:44,621] [INFO] Running command: cat /var/lib/cwl/stg03d9de8d-58be-4e27-adef-fbed12e0c03d/OceanDNA-b2084.fa | prodigal -d OceanDNA-b2084/cds.fna -a OceanDNA-b2084/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:13:47,345] [INFO] Task succeeded: Prodigal
[2023-03-14 12:13:47,345] [INFO] Task started: HMMsearch
[2023-03-14 12:13:47,345] [INFO] Running command: hmmsearch --tblout OceanDNA-b2084/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c8eb785-69b9-48f0-888b-a37db6c62b96/dqc_reference/reference_markers.hmm OceanDNA-b2084/protein.faa > /dev/null
[2023-03-14 12:13:47,547] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:13:47,547] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg03d9de8d-58be-4e27-adef-fbed12e0c03d/OceanDNA-b2084.fa]
[2023-03-14 12:13:47,553] [INFO] Query marker FASTA was written to OceanDNA-b2084/markers.fasta
[2023-03-14 12:13:47,555] [INFO] Task started: Blastn
[2023-03-14 12:13:47,555] [INFO] Running command: blastn -query OceanDNA-b2084/markers.fasta -db /var/lib/cwl/stg6c8eb785-69b9-48f0-888b-a37db6c62b96/dqc_reference/reference_markers.fasta -out OceanDNA-b2084/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:13:50,813] [INFO] Task succeeded: Blastn
[2023-03-14 12:13:50,814] [INFO] Selected 7 target genomes.
[2023-03-14 12:13:50,814] [INFO] Target genome list was writen to OceanDNA-b2084/target_genomes.txt
[2023-03-14 12:13:50,819] [INFO] Task started: fastANI
[2023-03-14 12:13:50,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg03d9de8d-58be-4e27-adef-fbed12e0c03d/OceanDNA-b2084.fa --refList OceanDNA-b2084/target_genomes.txt --output OceanDNA-b2084/fastani_result.tsv --threads 1
[2023-03-14 12:13:53,695] [INFO] Task succeeded: fastANI
[2023-03-14 12:13:53,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c8eb785-69b9-48f0-888b-a37db6c62b96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:13:53,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c8eb785-69b9-48f0-888b-a37db6c62b96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:13:53,696] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:13:53,696] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:13:53,696] [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 12:13:53,696] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2084/tc_result.tsv
[2023-03-14 12:13:53,697] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:13:53,697] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:13:53,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c8eb785-69b9-48f0-888b-a37db6c62b96/dqc_reference/checkm_data
[2023-03-14 12:13:53,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:13:53,701] [INFO] Task started: CheckM
[2023-03-14 12:13:53,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2084/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2084/checkm_input OceanDNA-b2084/checkm_result
[2023-03-14 12:14:09,103] [INFO] Task succeeded: CheckM
[2023-03-14 12:14:09,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:14:09,105] [INFO] ===== Completeness check finished =====
[2023-03-14 12:14:09,105] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:14:09,105] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2084/markers.fasta)
[2023-03-14 12:14:09,106] [INFO] Task started: Blastn
[2023-03-14 12:14:09,106] [INFO] Running command: blastn -query OceanDNA-b2084/markers.fasta -db /var/lib/cwl/stg6c8eb785-69b9-48f0-888b-a37db6c62b96/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2084/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:14:09,922] [INFO] Task succeeded: Blastn
[2023-03-14 12:14:09,923] [INFO] Selected 20 target genomes.
[2023-03-14 12:14:09,923] [INFO] Target genome list was writen to OceanDNA-b2084/target_genomes_gtdb.txt
[2023-03-14 12:14:09,937] [INFO] Task started: fastANI
[2023-03-14 12:14:09,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg03d9de8d-58be-4e27-adef-fbed12e0c03d/OceanDNA-b2084.fa --refList OceanDNA-b2084/target_genomes_gtdb.txt --output OceanDNA-b2084/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:14:13,015] [INFO] Task succeeded: fastANI
[2023-03-14 12:14:13,020] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:14:13,020] [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_002169845.1	s__Actinomarina sp002169845	91.7612	93	162	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	82.5632	122	162	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	81.9858	96	162	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.49	98.44	0.76	0.76	3	-
GCA_014384285.1	s__Actinomarina sp014384285	80.2776	100	162	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	99.05	98.78	0.90	0.82	4	-
GCA_002308095.1	s__Actinomarina sp002308095	79.5969	74	162	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:14:13,020] [INFO] GTDB search result was written to OceanDNA-b2084/result_gtdb.tsv
[2023-03-14 12:14:13,020] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:14:13,021] [INFO] DFAST_QC result json was written to OceanDNA-b2084/dqc_result.json
[2023-03-14 12:14:13,021] [INFO] DFAST_QC completed!
[2023-03-14 12:14:13,021] [INFO] Total running time: 0h0m30s