[2023-06-08 14:46:48,268] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:46:48,280] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:46:48,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg63830164-4688-41fe-9ec5-07caf03b77eb/dqc_reference
[2023-06-08 14:46:49,935] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:46:49,936] [INFO] Task started: Prodigal
[2023-06-08 14:46:49,936] [INFO] Running command: gunzip -c /var/lib/cwl/stg40babf9b-62dc-461f-9638-2f0c53f5c05c/GCA_947486645.1_ZE-13oct10-122_genomic.fna.gz | prodigal -d GCA_947486645.1_ZE-13oct10-122_genomic.fna/cds.fna -a GCA_947486645.1_ZE-13oct10-122_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:46:54,607] [INFO] Task succeeded: Prodigal
[2023-06-08 14:46:54,607] [INFO] Task started: HMMsearch
[2023-06-08 14:46:54,607] [INFO] Running command: hmmsearch --tblout GCA_947486645.1_ZE-13oct10-122_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63830164-4688-41fe-9ec5-07caf03b77eb/dqc_reference/reference_markers.hmm GCA_947486645.1_ZE-13oct10-122_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:46:54,820] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:46:54,822] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg40babf9b-62dc-461f-9638-2f0c53f5c05c/GCA_947486645.1_ZE-13oct10-122_genomic.fna.gz]
[2023-06-08 14:46:54,839] [INFO] Query marker FASTA was written to GCA_947486645.1_ZE-13oct10-122_genomic.fna/markers.fasta
[2023-06-08 14:46:54,840] [INFO] Task started: Blastn
[2023-06-08 14:46:54,840] [INFO] Running command: blastn -query GCA_947486645.1_ZE-13oct10-122_genomic.fna/markers.fasta -db /var/lib/cwl/stg63830164-4688-41fe-9ec5-07caf03b77eb/dqc_reference/reference_markers.fasta -out GCA_947486645.1_ZE-13oct10-122_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:46:55,395] [INFO] Task succeeded: Blastn
[2023-06-08 14:46:55,400] [INFO] Selected 14 target genomes.
[2023-06-08 14:46:55,400] [INFO] Target genome list was writen to GCA_947486645.1_ZE-13oct10-122_genomic.fna/target_genomes.txt
[2023-06-08 14:46:55,423] [INFO] Task started: fastANI
[2023-06-08 14:46:55,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg40babf9b-62dc-461f-9638-2f0c53f5c05c/GCA_947486645.1_ZE-13oct10-122_genomic.fna.gz --refList GCA_947486645.1_ZE-13oct10-122_genomic.fna/target_genomes.txt --output GCA_947486645.1_ZE-13oct10-122_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:47:02,784] [INFO] Task succeeded: fastANI
[2023-06-08 14:47:02,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63830164-4688-41fe-9ec5-07caf03b77eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:47:02,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63830164-4688-41fe-9ec5-07caf03b77eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:47:02,788] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:47:02,789] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 14:47:02,789] [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
--------------------------------------------------------------------------------
[2023-06-08 14:47:02,794] [INFO] DFAST Taxonomy check result was written to GCA_947486645.1_ZE-13oct10-122_genomic.fna/tc_result.tsv
[2023-06-08 14:47:02,796] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:47:02,796] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:47:02,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63830164-4688-41fe-9ec5-07caf03b77eb/dqc_reference/checkm_data
[2023-06-08 14:47:02,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:47:02,825] [INFO] Task started: CheckM
[2023-06-08 14:47:02,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947486645.1_ZE-13oct10-122_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947486645.1_ZE-13oct10-122_genomic.fna/checkm_input GCA_947486645.1_ZE-13oct10-122_genomic.fna/checkm_result
[2023-06-08 14:47:24,292] [INFO] Task succeeded: CheckM
[2023-06-08 14:47:24,294] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.97%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:47:24,320] [INFO] ===== Completeness check finished =====
[2023-06-08 14:47:24,320] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:47:24,321] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947486645.1_ZE-13oct10-122_genomic.fna/markers.fasta)
[2023-06-08 14:47:24,321] [INFO] Task started: Blastn
[2023-06-08 14:47:24,321] [INFO] Running command: blastn -query GCA_947486645.1_ZE-13oct10-122_genomic.fna/markers.fasta -db /var/lib/cwl/stg63830164-4688-41fe-9ec5-07caf03b77eb/dqc_reference/reference_markers_gtdb.fasta -out GCA_947486645.1_ZE-13oct10-122_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:47:25,086] [INFO] Task succeeded: Blastn
[2023-06-08 14:47:25,089] [INFO] Selected 12 target genomes.
[2023-06-08 14:47:25,090] [INFO] Target genome list was writen to GCA_947486645.1_ZE-13oct10-122_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:47:25,096] [INFO] Task started: fastANI
[2023-06-08 14:47:25,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg40babf9b-62dc-461f-9638-2f0c53f5c05c/GCA_947486645.1_ZE-13oct10-122_genomic.fna.gz --refList GCA_947486645.1_ZE-13oct10-122_genomic.fna/target_genomes_gtdb.txt --output GCA_947486645.1_ZE-13oct10-122_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:47:28,948] [INFO] Task succeeded: fastANI
[2023-06-08 14:47:28,964] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 14:47:28,965] [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_005788815.1	s__UBA2093 sp005788815	89.8326	317	448	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934195.1	s__UBA2093 sp903934195	79.2854	105	448	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929185.1	s__UBA2093 sp903929185	78.5147	136	448	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	98.72	96.70	0.83	0.75	5	-
GCA_009704065.1	s__UBA2093 sp009704065	78.4635	108	448	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	98.28	98.28	0.82	0.82	2	-
GCA_009694565.1	s__UBA2093 sp009694565	78.3975	136	448	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009705865.1	s__UBA2093 sp009705865	78.2787	130	448	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	99.12	99.02	0.86	0.85	3	-
GCA_903904615.1	s__UBA2093 sp903904615	78.1618	104	448	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702755.1	s__UBA2093 sp009702755	77.9838	124	448	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009703055.1	s__UBA2093 sp009703055	77.7537	102	448	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009703125.1	s__UBA2093 sp009703125	77.2907	99	448	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	98.43	98.43	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-08 14:47:28,966] [INFO] GTDB search result was written to GCA_947486645.1_ZE-13oct10-122_genomic.fna/result_gtdb.tsv
[2023-06-08 14:47:28,967] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:47:28,970] [INFO] DFAST_QC result json was written to GCA_947486645.1_ZE-13oct10-122_genomic.fna/dqc_result.json
[2023-06-08 14:47:28,970] [INFO] DFAST_QC completed!
[2023-06-08 14:47:28,970] [INFO] Total running time: 0h0m41s