[2023-06-08 13:03:42,815] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:03:42,819] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:03:42,819] [INFO] DQC Reference Directory: /var/lib/cwl/stg1abb332f-233b-4576-a91c-21f9cd851e52/dqc_reference
[2023-06-08 13:03:45,282] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:03:45,283] [INFO] Task started: Prodigal
[2023-06-08 13:03:45,283] [INFO] Running command: gunzip -c /var/lib/cwl/stge5373099-89fc-47b6-9ffa-3ca933fdb409/GCA_945863785.1_MiE-16apr19-309_genomic.fna.gz | prodigal -d GCA_945863785.1_MiE-16apr19-309_genomic.fna/cds.fna -a GCA_945863785.1_MiE-16apr19-309_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:03:55,427] [INFO] Task succeeded: Prodigal
[2023-06-08 13:03:55,427] [INFO] Task started: HMMsearch
[2023-06-08 13:03:55,427] [INFO] Running command: hmmsearch --tblout GCA_945863785.1_MiE-16apr19-309_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1abb332f-233b-4576-a91c-21f9cd851e52/dqc_reference/reference_markers.hmm GCA_945863785.1_MiE-16apr19-309_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:03:55,565] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:03:55,566] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge5373099-89fc-47b6-9ffa-3ca933fdb409/GCA_945863785.1_MiE-16apr19-309_genomic.fna.gz]
[2023-06-08 13:03:55,591] [INFO] Query marker FASTA was written to GCA_945863785.1_MiE-16apr19-309_genomic.fna/markers.fasta
[2023-06-08 13:03:55,591] [INFO] Task started: Blastn
[2023-06-08 13:03:55,591] [INFO] Running command: blastn -query GCA_945863785.1_MiE-16apr19-309_genomic.fna/markers.fasta -db /var/lib/cwl/stg1abb332f-233b-4576-a91c-21f9cd851e52/dqc_reference/reference_markers.fasta -out GCA_945863785.1_MiE-16apr19-309_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:03:56,127] [INFO] Task succeeded: Blastn
[2023-06-08 13:03:56,131] [INFO] Selected 10 target genomes.
[2023-06-08 13:03:56,132] [INFO] Target genome list was writen to GCA_945863785.1_MiE-16apr19-309_genomic.fna/target_genomes.txt
[2023-06-08 13:03:56,133] [INFO] Task started: fastANI
[2023-06-08 13:03:56,133] [INFO] Running command: fastANI --query /var/lib/cwl/stge5373099-89fc-47b6-9ffa-3ca933fdb409/GCA_945863785.1_MiE-16apr19-309_genomic.fna.gz --refList GCA_945863785.1_MiE-16apr19-309_genomic.fna/target_genomes.txt --output GCA_945863785.1_MiE-16apr19-309_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:04:02,009] [INFO] Task succeeded: fastANI
[2023-06-08 13:04:02,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1abb332f-233b-4576-a91c-21f9cd851e52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:04:02,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1abb332f-233b-4576-a91c-21f9cd851e52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:04:02,012] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:04:02,012] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 13:04:02,012] [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 13:04:02,014] [INFO] DFAST Taxonomy check result was written to GCA_945863785.1_MiE-16apr19-309_genomic.fna/tc_result.tsv
[2023-06-08 13:04:02,014] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:04:02,014] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:04:02,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1abb332f-233b-4576-a91c-21f9cd851e52/dqc_reference/checkm_data
[2023-06-08 13:04:02,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:04:02,037] [INFO] Task started: CheckM
[2023-06-08 13:04:02,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945863785.1_MiE-16apr19-309_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945863785.1_MiE-16apr19-309_genomic.fna/checkm_input GCA_945863785.1_MiE-16apr19-309_genomic.fna/checkm_result
[2023-06-08 13:04:35,068] [INFO] Task succeeded: CheckM
[2023-06-08 13:04:35,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:04:35,088] [INFO] ===== Completeness check finished =====
[2023-06-08 13:04:35,088] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:04:35,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945863785.1_MiE-16apr19-309_genomic.fna/markers.fasta)
[2023-06-08 13:04:35,089] [INFO] Task started: Blastn
[2023-06-08 13:04:35,089] [INFO] Running command: blastn -query GCA_945863785.1_MiE-16apr19-309_genomic.fna/markers.fasta -db /var/lib/cwl/stg1abb332f-233b-4576-a91c-21f9cd851e52/dqc_reference/reference_markers_gtdb.fasta -out GCA_945863785.1_MiE-16apr19-309_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:04:35,798] [INFO] Task succeeded: Blastn
[2023-06-08 13:04:35,802] [INFO] Selected 12 target genomes.
[2023-06-08 13:04:35,802] [INFO] Target genome list was writen to GCA_945863785.1_MiE-16apr19-309_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:04:35,875] [INFO] Task started: fastANI
[2023-06-08 13:04:35,876] [INFO] Running command: fastANI --query /var/lib/cwl/stge5373099-89fc-47b6-9ffa-3ca933fdb409/GCA_945863785.1_MiE-16apr19-309_genomic.fna.gz --refList GCA_945863785.1_MiE-16apr19-309_genomic.fna/target_genomes_gtdb.txt --output GCA_945863785.1_MiE-16apr19-309_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:04:40,944] [INFO] Task succeeded: fastANI
[2023-06-08 13:04:40,951] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 13:04:40,951] [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_009920585.1	s__UBA967 sp009920585	92.6704	355	519	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	99.04	99.04	0.77	0.77	2	-
GCA_903915315.1	s__UBA967 sp903915315	85.7739	275	519	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886045.1	s__UBA967 sp009886045	77.1827	80	519	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402345.1	s__UBA967 sp018402345	77.0238	81	519	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002290555.1	s__UBA967 sp002290555	76.7963	63	519	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	99.67	99.67	0.84	0.84	2	-
GCA_002396485.1	s__UBA967 sp002396485	76.7746	104	519	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 13:04:40,953] [INFO] GTDB search result was written to GCA_945863785.1_MiE-16apr19-309_genomic.fna/result_gtdb.tsv
[2023-06-08 13:04:40,954] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:04:40,956] [INFO] DFAST_QC result json was written to GCA_945863785.1_MiE-16apr19-309_genomic.fna/dqc_result.json
[2023-06-08 13:04:40,956] [INFO] DFAST_QC completed!
[2023-06-08 13:04:40,956] [INFO] Total running time: 0h0m58s