[2023-03-17 22:57:28,031] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:57:28,031] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:57:28,031] [INFO] DQC Reference Directory: /var/lib/cwl/stg3898e3df-aa12-4098-82e2-56ad3708f636/dqc_reference
[2023-03-17 22:57:29,173] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:57:29,174] [INFO] Task started: Prodigal
[2023-03-17 22:57:29,174] [INFO] Running command: cat /var/lib/cwl/stgc249dba1-8009-43e7-889c-e735edc2ac53/OceanDNA-b22759.fa | prodigal -d OceanDNA-b22759/cds.fna -a OceanDNA-b22759/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:57:43,301] [INFO] Task succeeded: Prodigal
[2023-03-17 22:57:43,301] [INFO] Task started: HMMsearch
[2023-03-17 22:57:43,301] [INFO] Running command: hmmsearch --tblout OceanDNA-b22759/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3898e3df-aa12-4098-82e2-56ad3708f636/dqc_reference/reference_markers.hmm OceanDNA-b22759/protein.faa > /dev/null
[2023-03-17 22:57:43,475] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:57:43,475] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc249dba1-8009-43e7-889c-e735edc2ac53/OceanDNA-b22759.fa]
[2023-03-17 22:57:43,494] [INFO] Query marker FASTA was written to OceanDNA-b22759/markers.fasta
[2023-03-17 22:57:43,496] [INFO] Task started: Blastn
[2023-03-17 22:57:43,496] [INFO] Running command: blastn -query OceanDNA-b22759/markers.fasta -db /var/lib/cwl/stg3898e3df-aa12-4098-82e2-56ad3708f636/dqc_reference/reference_markers.fasta -out OceanDNA-b22759/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:57:44,076] [INFO] Task succeeded: Blastn
[2023-03-17 22:57:44,079] [INFO] Selected 7 target genomes.
[2023-03-17 22:57:44,079] [INFO] Target genome list was writen to OceanDNA-b22759/target_genomes.txt
[2023-03-17 22:57:44,085] [INFO] Task started: fastANI
[2023-03-17 22:57:44,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgc249dba1-8009-43e7-889c-e735edc2ac53/OceanDNA-b22759.fa --refList OceanDNA-b22759/target_genomes.txt --output OceanDNA-b22759/fastani_result.tsv --threads 1
[2023-03-17 22:57:47,741] [INFO] Task succeeded: fastANI
[2023-03-17 22:57:47,742] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3898e3df-aa12-4098-82e2-56ad3708f636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:57:47,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3898e3df-aa12-4098-82e2-56ad3708f636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:57:47,742] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:57:47,742] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 22:57:47,742] [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
--------------------------------------------------------------------------------
[2023-03-17 22:57:47,744] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22759/tc_result.tsv
[2023-03-17 22:57:47,745] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:57:47,745] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:57:47,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3898e3df-aa12-4098-82e2-56ad3708f636/dqc_reference/checkm_data
[2023-03-17 22:57:47,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:57:47,931] [INFO] Task started: CheckM
[2023-03-17 22:57:47,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22759/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22759/checkm_input OceanDNA-b22759/checkm_result
[2023-03-17 22:58:27,375] [INFO] Task succeeded: CheckM
[2023-03-17 22:58:27,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 22:58:27,377] [INFO] ===== Completeness check finished =====
[2023-03-17 22:58:27,377] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:58:27,377] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22759/markers.fasta)
[2023-03-17 22:58:27,379] [INFO] Task started: Blastn
[2023-03-17 22:58:27,379] [INFO] Running command: blastn -query OceanDNA-b22759/markers.fasta -db /var/lib/cwl/stg3898e3df-aa12-4098-82e2-56ad3708f636/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22759/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:58:28,488] [INFO] Task succeeded: Blastn
[2023-03-17 22:58:28,489] [INFO] Selected 8 target genomes.
[2023-03-17 22:58:28,489] [INFO] Target genome list was writen to OceanDNA-b22759/target_genomes_gtdb.txt
[2023-03-17 22:58:28,498] [INFO] Task started: fastANI
[2023-03-17 22:58:28,498] [INFO] Running command: fastANI --query /var/lib/cwl/stgc249dba1-8009-43e7-889c-e735edc2ac53/OceanDNA-b22759.fa --refList OceanDNA-b22759/target_genomes_gtdb.txt --output OceanDNA-b22759/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:58:33,020] [INFO] Task succeeded: fastANI
[2023-03-17 22:58:33,027] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 22:58:33,027] [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_003509235.1	s__UBA1268 sp003509235	99.1751	539	779	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905477565.1	s__UBA1268 sp905477565	87.2681	318	779	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016776925.1	s__UBA1268 sp016776925	85.8195	615	779	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	98.79	96.90	0.88	0.85	13	-
GCA_002694955.1	s__UBA1268 sp002694955	82.2435	266	779	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	98.59	98.49	0.92	0.91	3	-
GCA_018694455.1	s__UBA1268 sp018694455	79.2827	326	779	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	98.79	98.58	0.79	0.76	6	-
GCA_002862165.1	s__UBA1268 sp002862165	78.8378	246	779	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238855.1	s__UBA1268 sp014238855	78.7973	322	779	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:58:33,027] [INFO] GTDB search result was written to OceanDNA-b22759/result_gtdb.tsv
[2023-03-17 22:58:33,027] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:58:33,028] [INFO] DFAST_QC result json was written to OceanDNA-b22759/dqc_result.json
[2023-03-17 22:58:33,028] [INFO] DFAST_QC completed!
[2023-03-17 22:58:33,028] [INFO] Total running time: 0h1m5s