[2023-03-15 12:33:51,636] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,636] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,636] [INFO] DQC Reference Directory: /var/lib/cwl/stg83112143-9683-4b9e-baed-7e9dbe3348df/dqc_reference
[2023-03-15 12:33:52,742] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,743] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,743] [INFO] Running command: cat /var/lib/cwl/stg1a62663d-58e1-472a-a67b-67b25d111ea6/OceanDNA-b2483.fa | prodigal -d OceanDNA-b2483/cds.fna -a OceanDNA-b2483/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:33:56,338] [INFO] Task succeeded: Prodigal
[2023-03-15 12:33:56,339] [INFO] Task started: HMMsearch
[2023-03-15 12:33:56,339] [INFO] Running command: hmmsearch --tblout OceanDNA-b2483/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83112143-9683-4b9e-baed-7e9dbe3348df/dqc_reference/reference_markers.hmm OceanDNA-b2483/protein.faa > /dev/null
[2023-03-15 12:33:56,523] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:33:56,523] [INFO] Found 6/6 markers.
[2023-03-15 12:33:56,532] [INFO] Query marker FASTA was written to OceanDNA-b2483/markers.fasta
[2023-03-15 12:33:56,533] [INFO] Task started: Blastn
[2023-03-15 12:33:56,533] [INFO] Running command: blastn -query OceanDNA-b2483/markers.fasta -db /var/lib/cwl/stg83112143-9683-4b9e-baed-7e9dbe3348df/dqc_reference/reference_markers.fasta -out OceanDNA-b2483/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:33:57,248] [INFO] Task succeeded: Blastn
[2023-03-15 12:33:57,250] [INFO] Selected 7 target genomes.
[2023-03-15 12:33:57,250] [INFO] Target genome list was writen to OceanDNA-b2483/target_genomes.txt
[2023-03-15 12:33:57,255] [INFO] Task started: fastANI
[2023-03-15 12:33:57,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a62663d-58e1-472a-a67b-67b25d111ea6/OceanDNA-b2483.fa --refList OceanDNA-b2483/target_genomes.txt --output OceanDNA-b2483/fastani_result.tsv --threads 1
[2023-03-15 12:34:00,026] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:00,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83112143-9683-4b9e-baed-7e9dbe3348df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:00,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83112143-9683-4b9e-baed-7e9dbe3348df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:00,027] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:00,027] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:34:00,027] [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
--------------------------------------------------------------------------------
[2023-03-15 12:34:00,028] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2483/tc_result.tsv
[2023-03-15 12:34:00,028] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:00,028] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:00,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83112143-9683-4b9e-baed-7e9dbe3348df/dqc_reference/checkm_data
[2023-03-15 12:34:00,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:00,085] [INFO] Task started: CheckM
[2023-03-15 12:34:00,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2483/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2483/checkm_input OceanDNA-b2483/checkm_result
[2023-03-15 12:34:19,643] [INFO] Task succeeded: CheckM
[2023-03-15 12:34:19,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 5.39%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-15 12:34:19,649] [INFO] ===== Completeness check finished =====
[2023-03-15 12:34:19,650] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:34:19,650] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2483/markers.fasta)
[2023-03-15 12:34:19,650] [INFO] Task started: Blastn
[2023-03-15 12:34:19,650] [INFO] Running command: blastn -query OceanDNA-b2483/markers.fasta -db /var/lib/cwl/stg83112143-9683-4b9e-baed-7e9dbe3348df/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2483/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:20,849] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:20,852] [INFO] Selected 14 target genomes.
[2023-03-15 12:34:20,852] [INFO] Target genome list was writen to OceanDNA-b2483/target_genomes_gtdb.txt
[2023-03-15 12:34:20,979] [INFO] Task started: fastANI
[2023-03-15 12:34:20,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a62663d-58e1-472a-a67b-67b25d111ea6/OceanDNA-b2483.fa --refList OceanDNA-b2483/target_genomes_gtdb.txt --output OceanDNA-b2483/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:34:23,569] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:23,574] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:34:23,575] [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_003282445.1	s__Actinomarina sp003282445	97.2801	194	202	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.01	96.02	0.90	0.85	11	conclusive
GCA_002724835.1	s__Actinomarina sp002724835	93.0951	173	202	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.97	95.84	0.72	0.71	4	-
GCA_004214055.1	s__Actinomarina sp004214055	84.489	131	202	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510995.1	s__Actinomarina sp902510995	83.4975	141	202	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.36	95.36	0.76	0.76	2	-
GCA_902565645.1	s__Actinomarina sp902565645	80.9073	119	202	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902571385.1	s__Actinomarina sp902571385	77.2881	56	202	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.95	95.63	0.85	0.83	4	-
GCA_003213625.1	s__Actinomarina sp003213625	77.1022	61	202	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.18	95.09	0.86	0.82	29	-
GCA_902533795.1	s__Actinomarina sp902533795	76.874	67	202	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.75	95.75	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-15 12:34:23,576] [INFO] GTDB search result was written to OceanDNA-b2483/result_gtdb.tsv
[2023-03-15 12:34:23,576] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:34:23,577] [INFO] DFAST_QC result json was written to OceanDNA-b2483/dqc_result.json
[2023-03-15 12:34:23,577] [INFO] DFAST_QC completed!
[2023-03-15 12:34:23,577] [INFO] Total running time: 0h0m32s