[2023-06-28 01:17:32,856] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:17:32,858] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:17:32,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg31dfb38e-1f33-46c7-98ab-1d62b164e9bf/dqc_reference
[2023-06-28 01:17:34,882] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:17:34,882] [INFO] Task started: Prodigal
[2023-06-28 01:17:34,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg63540f64-83f4-4b42-832e-3fe631830d38/GCA_017997415.1_ASM1799741v1_genomic.fna.gz | prodigal -d GCA_017997415.1_ASM1799741v1_genomic.fna/cds.fna -a GCA_017997415.1_ASM1799741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:17:49,672] [INFO] Task succeeded: Prodigal
[2023-06-28 01:17:49,672] [INFO] Task started: HMMsearch
[2023-06-28 01:17:49,672] [INFO] Running command: hmmsearch --tblout GCA_017997415.1_ASM1799741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31dfb38e-1f33-46c7-98ab-1d62b164e9bf/dqc_reference/reference_markers.hmm GCA_017997415.1_ASM1799741v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:17:49,891] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:17:49,893] [INFO] Found 6/6 markers.
[2023-06-28 01:17:49,930] [INFO] Query marker FASTA was written to GCA_017997415.1_ASM1799741v1_genomic.fna/markers.fasta
[2023-06-28 01:17:49,931] [INFO] Task started: Blastn
[2023-06-28 01:17:49,931] [INFO] Running command: blastn -query GCA_017997415.1_ASM1799741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31dfb38e-1f33-46c7-98ab-1d62b164e9bf/dqc_reference/reference_markers.fasta -out GCA_017997415.1_ASM1799741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:17:50,583] [INFO] Task succeeded: Blastn
[2023-06-28 01:17:50,587] [INFO] Selected 31 target genomes.
[2023-06-28 01:17:50,587] [INFO] Target genome list was writen to GCA_017997415.1_ASM1799741v1_genomic.fna/target_genomes.txt
[2023-06-28 01:17:50,591] [INFO] Task started: fastANI
[2023-06-28 01:17:50,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg63540f64-83f4-4b42-832e-3fe631830d38/GCA_017997415.1_ASM1799741v1_genomic.fna.gz --refList GCA_017997415.1_ASM1799741v1_genomic.fna/target_genomes.txt --output GCA_017997415.1_ASM1799741v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:18:09,131] [INFO] Task succeeded: fastANI
[2023-06-28 01:18:09,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31dfb38e-1f33-46c7-98ab-1d62b164e9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:18:09,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31dfb38e-1f33-46c7-98ab-1d62b164e9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:18:09,136] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:18:09,136] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 01:18:09,136] [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
Methylobacterium segetis	strain=17J42-1	GCA_004348265.1	2488750	2488750	type	True	74.8779	52	1640	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	74.7155	64	1640	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:18:09,138] [INFO] DFAST Taxonomy check result was written to GCA_017997415.1_ASM1799741v1_genomic.fna/tc_result.tsv
[2023-06-28 01:18:09,139] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:18:09,139] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:18:09,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31dfb38e-1f33-46c7-98ab-1d62b164e9bf/dqc_reference/checkm_data
[2023-06-28 01:18:09,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:18:09,189] [INFO] Task started: CheckM
[2023-06-28 01:18:09,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017997415.1_ASM1799741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017997415.1_ASM1799741v1_genomic.fna/checkm_input GCA_017997415.1_ASM1799741v1_genomic.fna/checkm_result
[2023-06-28 01:18:52,890] [INFO] Task succeeded: CheckM
[2023-06-28 01:18:52,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 01:18:52,908] [INFO] ===== Completeness check finished =====
[2023-06-28 01:18:52,909] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:18:52,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017997415.1_ASM1799741v1_genomic.fna/markers.fasta)
[2023-06-28 01:18:52,909] [INFO] Task started: Blastn
[2023-06-28 01:18:52,909] [INFO] Running command: blastn -query GCA_017997415.1_ASM1799741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31dfb38e-1f33-46c7-98ab-1d62b164e9bf/dqc_reference/reference_markers_gtdb.fasta -out GCA_017997415.1_ASM1799741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:18:54,025] [INFO] Task succeeded: Blastn
[2023-06-28 01:18:54,029] [INFO] Selected 21 target genomes.
[2023-06-28 01:18:54,029] [INFO] Target genome list was writen to GCA_017997415.1_ASM1799741v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:18:54,035] [INFO] Task started: fastANI
[2023-06-28 01:18:54,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg63540f64-83f4-4b42-832e-3fe631830d38/GCA_017997415.1_ASM1799741v1_genomic.fna.gz --refList GCA_017997415.1_ASM1799741v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017997415.1_ASM1799741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:19:09,589] [INFO] Task succeeded: fastANI
[2023-06-28 01:19:09,600] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 01:19:09,601] [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_012719295.1	s__UBA2224 sp012719295	99.4937	1163	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__SLHB01;g__UBA2224	95.0	99.66	99.66	0.94	0.94	2	conclusive
GCA_002348185.1	s__UBA2224 sp002348185	90.855	1280	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__SLHB01;g__UBA2224	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007130675.1	s__UBA2224 sp007130675	76.6927	261	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__SLHB01;g__UBA2224	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422525.1	s__UBA6118 sp002422525	76.0414	116	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__SLHB01;g__UBA6118	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016934125.1	s__JAFGTL01 sp016934125	75.965	153	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__SLHB01;g__JAFGTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018005585.1	s__JAGMZX01 sp018005585	75.9557	126	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__JAGMZX01;g__JAGMZX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011682535.1	s__JAACEL01 sp011682535	75.9142	86	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__SLHB01;g__JAACEL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730045.1	s__JAAYBR01 sp012730045	75.7648	110	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__CAITNO01;g__JAAYBR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893795.1	s__CAITNO01 sp903893795	75.702	91	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__CAITNO01;g__CAITNO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011328705.1	s__DSVR01 sp011328705	75.6225	77	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__SLHB01;g__DSVR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125095.1	s__WGMK01 sp016125095	75.5851	88	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__WGMK01;g__WGMK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013359265.1	s__JABWCD01 sp013359265	75.5521	95	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__SLHB01;g__JABWCD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791475.1	s__JAEUWI01 sp016791475	75.3827	81	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__WGMK01;g__JAEUWI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730105.1	s__JAAYBJ01 sp012730105	75.2377	82	1640	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__CAITNO01;g__JAAYBJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:19:09,602] [INFO] GTDB search result was written to GCA_017997415.1_ASM1799741v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:19:09,603] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:19:09,605] [INFO] DFAST_QC result json was written to GCA_017997415.1_ASM1799741v1_genomic.fna/dqc_result.json
[2023-06-28 01:19:09,606] [INFO] DFAST_QC completed!
[2023-06-28 01:19:09,606] [INFO] Total running time: 0h1m37s