[2023-03-15 14:06:11,244] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:06:11,244] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:06:11,244] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3229bde-dc2d-4437-b246-e48fb1e46d99/dqc_reference
[2023-03-15 14:06:12,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:06:12,360] [INFO] Task started: Prodigal
[2023-03-15 14:06:12,360] [INFO] Running command: cat /var/lib/cwl/stgd2c7d204-2c01-44a6-a5ad-dd1f2a074898/OceanDNA-a549.fa | prodigal -d OceanDNA-a549/cds.fna -a OceanDNA-a549/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:06:16,756] [INFO] Task succeeded: Prodigal
[2023-03-15 14:06:16,756] [INFO] Task started: HMMsearch
[2023-03-15 14:06:16,756] [INFO] Running command: hmmsearch --tblout OceanDNA-a549/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3229bde-dc2d-4437-b246-e48fb1e46d99/dqc_reference/reference_markers.hmm OceanDNA-a549/protein.faa > /dev/null
[2023-03-15 14:06:16,887] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:06:16,887] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgd2c7d204-2c01-44a6-a5ad-dd1f2a074898/OceanDNA-a549.fa]
[2023-03-15 14:06:16,896] [INFO] Query marker FASTA was written to OceanDNA-a549/markers.fasta
[2023-03-15 14:06:16,897] [INFO] Task started: Blastn
[2023-03-15 14:06:16,897] [INFO] Running command: blastn -query OceanDNA-a549/markers.fasta -db /var/lib/cwl/stgc3229bde-dc2d-4437-b246-e48fb1e46d99/dqc_reference/reference_markers.fasta -out OceanDNA-a549/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:06:17,360] [INFO] Task succeeded: Blastn
[2023-03-15 14:06:17,361] [INFO] Selected 3 target genomes.
[2023-03-15 14:06:17,361] [INFO] Target genome list was writen to OceanDNA-a549/target_genomes.txt
[2023-03-15 14:06:17,364] [INFO] Task started: fastANI
[2023-03-15 14:06:17,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2c7d204-2c01-44a6-a5ad-dd1f2a074898/OceanDNA-a549.fa --refList OceanDNA-a549/target_genomes.txt --output OceanDNA-a549/fastani_result.tsv --threads 1
[2023-03-15 14:06:18,346] [INFO] Task succeeded: fastANI
[2023-03-15 14:06:18,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3229bde-dc2d-4437-b246-e48fb1e46d99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:06:18,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3229bde-dc2d-4437-b246-e48fb1e46d99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:06:18,397] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:06:18,397] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:06:18,397] [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
Nitrosopumilus cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	81.4357	214	266	95	below_threshold
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	81.367	218	266	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	80.6935	201	266	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:06:18,398] [INFO] DFAST Taxonomy check result was written to OceanDNA-a549/tc_result.tsv
[2023-03-15 14:06:18,398] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:06:18,398] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:06:18,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3229bde-dc2d-4437-b246-e48fb1e46d99/dqc_reference/checkm_data
[2023-03-15 14:06:18,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:06:18,613] [INFO] Task started: CheckM
[2023-03-15 14:06:18,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a549/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a549/checkm_input OceanDNA-a549/checkm_result
[2023-03-15 14:06:37,517] [INFO] Task succeeded: CheckM
[2023-03-15 14:06:37,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.57%
Contamintation: 1.45%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 14:06:37,521] [INFO] ===== Completeness check finished =====
[2023-03-15 14:06:37,521] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:06:37,521] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a549/markers.fasta)
[2023-03-15 14:06:37,522] [INFO] Task started: Blastn
[2023-03-15 14:06:37,523] [INFO] Running command: blastn -query OceanDNA-a549/markers.fasta -db /var/lib/cwl/stgc3229bde-dc2d-4437-b246-e48fb1e46d99/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a549/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:06:38,149] [INFO] Task succeeded: Blastn
[2023-03-15 14:06:38,151] [INFO] Selected 5 target genomes.
[2023-03-15 14:06:38,151] [INFO] Target genome list was writen to OceanDNA-a549/target_genomes_gtdb.txt
[2023-03-15 14:06:38,157] [INFO] Task started: fastANI
[2023-03-15 14:06:38,157] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2c7d204-2c01-44a6-a5ad-dd1f2a074898/OceanDNA-a549.fa --refList OceanDNA-a549/target_genomes_gtdb.txt --output OceanDNA-a549/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:06:39,195] [INFO] Task succeeded: fastANI
[2023-03-15 14:06:39,199] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:06:39,199] [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_018674605.1	s__Nitrosopumilus sp018674605	98.7043	157	266	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.83	98.50	0.79	0.69	12	conclusive
GCA_905616385.1	s__Nitrosopumilus sp905616385	87.776	135	266	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	97.32	96.75	0.55	0.53	3	-
GCA_902514095.1	s__Nitrosopumilus sp902514095	86.9899	159	266	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001437625.1	s__Nitrosopumilus sp001437625	86.648	198	266	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.62	95.42	0.85	0.75	5	-
GCA_905612295.1	s__Nitrosopumilus sp905612295	86.4592	156	266	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:06:39,200] [INFO] GTDB search result was written to OceanDNA-a549/result_gtdb.tsv
[2023-03-15 14:06:39,200] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:06:39,201] [INFO] DFAST_QC result json was written to OceanDNA-a549/dqc_result.json
[2023-03-15 14:06:39,202] [INFO] DFAST_QC completed!
[2023-03-15 14:06:39,202] [INFO] Total running time: 0h0m28s