[2023-06-28 08:44:09,209] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:44:09,211] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:44:09,211] [INFO] DQC Reference Directory: /var/lib/cwl/stg9be69f58-009e-4a57-a2b1-9f9c4d36804d/dqc_reference
[2023-06-28 08:44:10,404] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:44:10,405] [INFO] Task started: Prodigal
[2023-06-28 08:44:10,405] [INFO] Running command: gunzip -c /var/lib/cwl/stg33a9f1c1-b178-4600-8c69-eda43b352ac0/GCA_017882145.1_ASM1788214v1_genomic.fna.gz | prodigal -d GCA_017882145.1_ASM1788214v1_genomic.fna/cds.fna -a GCA_017882145.1_ASM1788214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:44:20,624] [INFO] Task succeeded: Prodigal
[2023-06-28 08:44:20,624] [INFO] Task started: HMMsearch
[2023-06-28 08:44:20,625] [INFO] Running command: hmmsearch --tblout GCA_017882145.1_ASM1788214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9be69f58-009e-4a57-a2b1-9f9c4d36804d/dqc_reference/reference_markers.hmm GCA_017882145.1_ASM1788214v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:44:20,862] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:44:20,863] [INFO] Found 6/6 markers.
[2023-06-28 08:44:20,897] [INFO] Query marker FASTA was written to GCA_017882145.1_ASM1788214v1_genomic.fna/markers.fasta
[2023-06-28 08:44:20,897] [INFO] Task started: Blastn
[2023-06-28 08:44:20,897] [INFO] Running command: blastn -query GCA_017882145.1_ASM1788214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9be69f58-009e-4a57-a2b1-9f9c4d36804d/dqc_reference/reference_markers.fasta -out GCA_017882145.1_ASM1788214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:44:21,461] [INFO] Task succeeded: Blastn
[2023-06-28 08:44:21,464] [INFO] Selected 22 target genomes.
[2023-06-28 08:44:21,465] [INFO] Target genome list was writen to GCA_017882145.1_ASM1788214v1_genomic.fna/target_genomes.txt
[2023-06-28 08:44:21,465] [INFO] Task started: fastANI
[2023-06-28 08:44:21,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg33a9f1c1-b178-4600-8c69-eda43b352ac0/GCA_017882145.1_ASM1788214v1_genomic.fna.gz --refList GCA_017882145.1_ASM1788214v1_genomic.fna/target_genomes.txt --output GCA_017882145.1_ASM1788214v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:44:34,039] [INFO] Task succeeded: fastANI
[2023-06-28 08:44:34,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9be69f58-009e-4a57-a2b1-9f9c4d36804d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:44:34,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9be69f58-009e-4a57-a2b1-9f9c4d36804d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:44:34,041] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:44:34,042] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 08:44:34,042] [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
--------------------------------------------------------------------------------
[2023-06-28 08:44:34,043] [INFO] DFAST Taxonomy check result was written to GCA_017882145.1_ASM1788214v1_genomic.fna/tc_result.tsv
[2023-06-28 08:44:34,044] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:44:34,044] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:44:34,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9be69f58-009e-4a57-a2b1-9f9c4d36804d/dqc_reference/checkm_data
[2023-06-28 08:44:34,047] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:44:34,087] [INFO] Task started: CheckM
[2023-06-28 08:44:34,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017882145.1_ASM1788214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017882145.1_ASM1788214v1_genomic.fna/checkm_input GCA_017882145.1_ASM1788214v1_genomic.fna/checkm_result
[2023-06-28 08:45:07,951] [INFO] Task succeeded: CheckM
[2023-06-28 08:45:07,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:45:07,967] [INFO] ===== Completeness check finished =====
[2023-06-28 08:45:07,968] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:45:07,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017882145.1_ASM1788214v1_genomic.fna/markers.fasta)
[2023-06-28 08:45:07,968] [INFO] Task started: Blastn
[2023-06-28 08:45:07,968] [INFO] Running command: blastn -query GCA_017882145.1_ASM1788214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9be69f58-009e-4a57-a2b1-9f9c4d36804d/dqc_reference/reference_markers_gtdb.fasta -out GCA_017882145.1_ASM1788214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:45:08,755] [INFO] Task succeeded: Blastn
[2023-06-28 08:45:08,760] [INFO] Selected 17 target genomes.
[2023-06-28 08:45:08,760] [INFO] Target genome list was writen to GCA_017882145.1_ASM1788214v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:45:08,761] [INFO] Task started: fastANI
[2023-06-28 08:45:08,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg33a9f1c1-b178-4600-8c69-eda43b352ac0/GCA_017882145.1_ASM1788214v1_genomic.fna.gz --refList GCA_017882145.1_ASM1788214v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017882145.1_ASM1788214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:45:16,841] [INFO] Task succeeded: fastANI
[2023-06-28 08:45:16,851] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 08:45:16,851] [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_017882145.1	s__UBA877 sp017882145	99.9999	1148	1165	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903873975.1	s__UBA877 sp903873975	77.7366	178	1165	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884265.1	s__UBA877 sp903884265	77.385	84	1165	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	99.41	99.41	0.88	0.88	2	-
GCA_017882125.1	s__UBA877 sp017882125	77.312	106	1165	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903829085.1	s__UBA877 sp903829085	77.1557	135	1165	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772985.1	s__UBA877 sp009772985	77.1345	152	1165	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882065.1	s__UBA877 sp017882065	77.0983	130	1165	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208355.1	s__UBA877 sp016208355	76.8685	120	1165	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016934715.1	s__JAFGSI01 sp016934715	76.4631	113	1165	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__JAFGSI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016865985.1	s__VGNO01 sp016865985	76.3729	80	1165	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__VGNO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 08:45:16,853] [INFO] GTDB search result was written to GCA_017882145.1_ASM1788214v1_genomic.fna/result_gtdb.tsv
[2023-06-28 08:45:16,853] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:45:16,856] [INFO] DFAST_QC result json was written to GCA_017882145.1_ASM1788214v1_genomic.fna/dqc_result.json
[2023-06-28 08:45:16,856] [INFO] DFAST_QC completed!
[2023-06-28 08:45:16,856] [INFO] Total running time: 0h1m8s