[2023-03-15 11:22:20,198] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:22:20,205] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:22:20,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg35c36127-8958-4f3b-a623-c14f1c49a973/dqc_reference
[2023-03-15 11:22:21,304] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:22:21,304] [INFO] Task started: Prodigal
[2023-03-15 11:22:21,304] [INFO] Running command: cat /var/lib/cwl/stg46a4ae3b-e543-4ce9-acc5-03736b61501c/OceanDNA-b46906.fa | prodigal -d OceanDNA-b46906/cds.fna -a OceanDNA-b46906/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:22:37,493] [INFO] Task succeeded: Prodigal
[2023-03-15 11:22:37,493] [INFO] Task started: HMMsearch
[2023-03-15 11:22:37,494] [INFO] Running command: hmmsearch --tblout OceanDNA-b46906/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35c36127-8958-4f3b-a623-c14f1c49a973/dqc_reference/reference_markers.hmm OceanDNA-b46906/protein.faa > /dev/null
[2023-03-15 11:22:37,676] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:22:37,677] [INFO] Found 6/6 markers.
[2023-03-15 11:22:37,709] [INFO] Query marker FASTA was written to OceanDNA-b46906/markers.fasta
[2023-03-15 11:22:37,710] [INFO] Task started: Blastn
[2023-03-15 11:22:37,710] [INFO] Running command: blastn -query OceanDNA-b46906/markers.fasta -db /var/lib/cwl/stg35c36127-8958-4f3b-a623-c14f1c49a973/dqc_reference/reference_markers.fasta -out OceanDNA-b46906/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:38,274] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:38,282] [INFO] Selected 22 target genomes.
[2023-03-15 11:22:38,283] [INFO] Target genome list was writen to OceanDNA-b46906/target_genomes.txt
[2023-03-15 11:22:38,296] [INFO] Task started: fastANI
[2023-03-15 11:22:38,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg46a4ae3b-e543-4ce9-acc5-03736b61501c/OceanDNA-b46906.fa --refList OceanDNA-b46906/target_genomes.txt --output OceanDNA-b46906/fastani_result.tsv --threads 1
[2023-03-15 11:22:52,493] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:52,494] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35c36127-8958-4f3b-a623-c14f1c49a973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:22:52,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35c36127-8958-4f3b-a623-c14f1c49a973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:22:52,494] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:22:52,494] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:22:52,494] [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 11:22:52,498] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46906/tc_result.tsv
[2023-03-15 11:22:52,501] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:22:52,501] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:22:52,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35c36127-8958-4f3b-a623-c14f1c49a973/dqc_reference/checkm_data
[2023-03-15 11:22:52,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:22:52,511] [INFO] Task started: CheckM
[2023-03-15 11:22:52,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46906/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46906/checkm_input OceanDNA-b46906/checkm_result
[2023-03-15 11:23:37,437] [INFO] Task succeeded: CheckM
[2023-03-15 11:23:37,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 2.23%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 11:23:37,468] [INFO] ===== Completeness check finished =====
[2023-03-15 11:23:37,468] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:23:37,468] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46906/markers.fasta)
[2023-03-15 11:23:37,469] [INFO] Task started: Blastn
[2023-03-15 11:23:37,469] [INFO] Running command: blastn -query OceanDNA-b46906/markers.fasta -db /var/lib/cwl/stg35c36127-8958-4f3b-a623-c14f1c49a973/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46906/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:23:38,208] [INFO] Task succeeded: Blastn
[2023-03-15 11:23:38,212] [INFO] Selected 16 target genomes.
[2023-03-15 11:23:38,212] [INFO] Target genome list was writen to OceanDNA-b46906/target_genomes_gtdb.txt
[2023-03-15 11:23:38,227] [INFO] Task started: fastANI
[2023-03-15 11:23:38,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg46a4ae3b-e543-4ce9-acc5-03736b61501c/OceanDNA-b46906.fa --refList OceanDNA-b46906/target_genomes_gtdb.txt --output OceanDNA-b46906/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:23:47,859] [INFO] Task succeeded: fastANI
[2023-03-15 11:23:47,863] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:23:47,863] [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_002292185.1	s__UBA985 sp002292185	99.0977	433	607	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	98.24	97.16	0.73	0.70	3	conclusive
GCA_017857425.1	s__UBA985 sp017857425	94.9931	446	607	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	96.59	96.59	0.83	0.83	2	-
GCA_009937455.1	s__UBA985 sp009937455	90.0055	420	607	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041925.1	s__UBA985 sp013041925	76.9232	99	607	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016811075.1	s__UBA985 sp016811075	76.8824	76	607	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	99.37	98.74	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2023-03-15 11:23:47,865] [INFO] GTDB search result was written to OceanDNA-b46906/result_gtdb.tsv
[2023-03-15 11:23:47,869] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:23:47,872] [INFO] DFAST_QC result json was written to OceanDNA-b46906/dqc_result.json
[2023-03-15 11:23:47,872] [INFO] DFAST_QC completed!
[2023-03-15 11:23:47,872] [INFO] Total running time: 0h1m28s