[2023-03-18 10:15:15,037] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:15:15,037] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:15:15,037] [INFO] DQC Reference Directory: /var/lib/cwl/stgab7f74d6-ae85-4354-9f03-7e0417fe075d/dqc_reference
[2023-03-18 10:15:16,171] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:15:16,172] [INFO] Task started: Prodigal
[2023-03-18 10:15:16,172] [INFO] Running command: cat /var/lib/cwl/stg74328005-44ec-4976-ab36-90c5a95992e4/OceanDNA-b2171.fa | prodigal -d OceanDNA-b2171/cds.fna -a OceanDNA-b2171/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:15:19,849] [INFO] Task succeeded: Prodigal
[2023-03-18 10:15:19,849] [INFO] Task started: HMMsearch
[2023-03-18 10:15:19,849] [INFO] Running command: hmmsearch --tblout OceanDNA-b2171/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab7f74d6-ae85-4354-9f03-7e0417fe075d/dqc_reference/reference_markers.hmm OceanDNA-b2171/protein.faa > /dev/null
[2023-03-18 10:15:20,009] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:15:20,009] [INFO] Found 6/6 markers.
[2023-03-18 10:15:20,016] [INFO] Query marker FASTA was written to OceanDNA-b2171/markers.fasta
[2023-03-18 10:15:20,017] [INFO] Task started: Blastn
[2023-03-18 10:15:20,017] [INFO] Running command: blastn -query OceanDNA-b2171/markers.fasta -db /var/lib/cwl/stgab7f74d6-ae85-4354-9f03-7e0417fe075d/dqc_reference/reference_markers.fasta -out OceanDNA-b2171/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:15:20,535] [INFO] Task succeeded: Blastn
[2023-03-18 10:15:20,535] [INFO] Selected 12 target genomes.
[2023-03-18 10:15:20,535] [INFO] Target genome list was writen to OceanDNA-b2171/target_genomes.txt
[2023-03-18 10:15:20,545] [INFO] Task started: fastANI
[2023-03-18 10:15:20,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg74328005-44ec-4976-ab36-90c5a95992e4/OceanDNA-b2171.fa --refList OceanDNA-b2171/target_genomes.txt --output OceanDNA-b2171/fastani_result.tsv --threads 1
[2023-03-18 10:15:24,818] [INFO] Task succeeded: fastANI
[2023-03-18 10:15:24,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab7f74d6-ae85-4354-9f03-7e0417fe075d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:15:24,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab7f74d6-ae85-4354-9f03-7e0417fe075d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:15:24,819] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:15:24,819] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:15:24,819] [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
--------------------------------------------------------------------------------
[2023-03-18 10:15:24,819] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2171/tc_result.tsv
[2023-03-18 10:15:24,819] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:15:24,819] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:15:24,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab7f74d6-ae85-4354-9f03-7e0417fe075d/dqc_reference/checkm_data
[2023-03-18 10:15:24,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:15:24,824] [INFO] Task started: CheckM
[2023-03-18 10:15:24,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2171/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2171/checkm_input OceanDNA-b2171/checkm_result
[2023-03-18 10:15:41,170] [INFO] Task succeeded: CheckM
[2023-03-18 10:15:41,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:15:41,172] [INFO] ===== Completeness check finished =====
[2023-03-18 10:15:41,172] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:15:41,172] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2171/markers.fasta)
[2023-03-18 10:15:41,173] [INFO] Task started: Blastn
[2023-03-18 10:15:41,174] [INFO] Running command: blastn -query OceanDNA-b2171/markers.fasta -db /var/lib/cwl/stgab7f74d6-ae85-4354-9f03-7e0417fe075d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2171/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:15:42,088] [INFO] Task succeeded: Blastn
[2023-03-18 10:15:42,089] [INFO] Selected 9 target genomes.
[2023-03-18 10:15:42,089] [INFO] Target genome list was writen to OceanDNA-b2171/target_genomes_gtdb.txt
[2023-03-18 10:15:42,099] [INFO] Task started: fastANI
[2023-03-18 10:15:42,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg74328005-44ec-4976-ab36-90c5a95992e4/OceanDNA-b2171.fa --refList OceanDNA-b2171/target_genomes_gtdb.txt --output OceanDNA-b2171/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:15:44,023] [INFO] Task succeeded: fastANI
[2023-03-18 10:15:44,028] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-18 10:15:44,028] [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_902596545.1	s__Actinomarina sp902596545	97.4419	213	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.42	98.42	0.93	0.93	2	inconclusive
GCA_902595195.1	s__Actinomarina sp902595195	97.1722	176	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.26	97.26	0.73	0.73	2	inconclusive
GCA_003281085.1	s__Actinomarina sp003281085	94.8202	182	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.17	95.08	0.82	0.73	10	-
GCA_003213165.1	s__Actinomarina sp003213165	89.4201	173	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.69	95.56	0.85	0.73	10	-
GCA_902625455.1	s__Actinomarina sp902625455	88.8569	204	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.46	97.35	0.85	0.81	4	-
GCA_902593475.1	s__Actinomarina sp902593475	79.5918	98	231	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:15:44,028] [INFO] GTDB search result was written to OceanDNA-b2171/result_gtdb.tsv
[2023-03-18 10:15:44,028] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:15:44,029] [INFO] DFAST_QC result json was written to OceanDNA-b2171/dqc_result.json
[2023-03-18 10:15:44,029] [INFO] DFAST_QC completed!
[2023-03-18 10:15:44,029] [INFO] Total running time: 0h0m29s