[2023-06-28 06:26:05,098] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:26:05,101] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:26:05,102] [INFO] DQC Reference Directory: /var/lib/cwl/stg02378f1f-856a-4da6-8bcc-c47356ffed1e/dqc_reference
[2023-06-28 06:26:06,305] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:26:06,306] [INFO] Task started: Prodigal
[2023-06-28 06:26:06,306] [INFO] Running command: gunzip -c /var/lib/cwl/stg96bc1cda-edce-4103-ad9a-54776fd81bc8/GCA_017416855.1_ASM1741685v1_genomic.fna.gz | prodigal -d GCA_017416855.1_ASM1741685v1_genomic.fna/cds.fna -a GCA_017416855.1_ASM1741685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:26:11,927] [INFO] Task succeeded: Prodigal
[2023-06-28 06:26:11,928] [INFO] Task started: HMMsearch
[2023-06-28 06:26:11,928] [INFO] Running command: hmmsearch --tblout GCA_017416855.1_ASM1741685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02378f1f-856a-4da6-8bcc-c47356ffed1e/dqc_reference/reference_markers.hmm GCA_017416855.1_ASM1741685v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:26:12,174] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:26:12,176] [INFO] Found 6/6 markers.
[2023-06-28 06:26:12,202] [INFO] Query marker FASTA was written to GCA_017416855.1_ASM1741685v1_genomic.fna/markers.fasta
[2023-06-28 06:26:12,203] [INFO] Task started: Blastn
[2023-06-28 06:26:12,203] [INFO] Running command: blastn -query GCA_017416855.1_ASM1741685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02378f1f-856a-4da6-8bcc-c47356ffed1e/dqc_reference/reference_markers.fasta -out GCA_017416855.1_ASM1741685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:26:12,837] [INFO] Task succeeded: Blastn
[2023-06-28 06:26:12,843] [INFO] Selected 29 target genomes.
[2023-06-28 06:26:12,844] [INFO] Target genome list was writen to GCA_017416855.1_ASM1741685v1_genomic.fna/target_genomes.txt
[2023-06-28 06:26:12,851] [INFO] Task started: fastANI
[2023-06-28 06:26:12,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg96bc1cda-edce-4103-ad9a-54776fd81bc8/GCA_017416855.1_ASM1741685v1_genomic.fna.gz --refList GCA_017416855.1_ASM1741685v1_genomic.fna/target_genomes.txt --output GCA_017416855.1_ASM1741685v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:26:26,336] [INFO] Task succeeded: fastANI
[2023-06-28 06:26:26,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02378f1f-856a-4da6-8bcc-c47356ffed1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:26:26,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02378f1f-856a-4da6-8bcc-c47356ffed1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:26:26,340] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:26:26,340] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 06:26:26,341] [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 06:26:26,343] [INFO] DFAST Taxonomy check result was written to GCA_017416855.1_ASM1741685v1_genomic.fna/tc_result.tsv
[2023-06-28 06:26:26,344] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:26:26,344] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:26:26,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02378f1f-856a-4da6-8bcc-c47356ffed1e/dqc_reference/checkm_data
[2023-06-28 06:26:26,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:26:26,382] [INFO] Task started: CheckM
[2023-06-28 06:26:26,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017416855.1_ASM1741685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017416855.1_ASM1741685v1_genomic.fna/checkm_input GCA_017416855.1_ASM1741685v1_genomic.fna/checkm_result
[2023-06-28 06:26:49,885] [INFO] Task succeeded: CheckM
[2023-06-28 06:26:49,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:26:49,909] [INFO] ===== Completeness check finished =====
[2023-06-28 06:26:49,910] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:26:49,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017416855.1_ASM1741685v1_genomic.fna/markers.fasta)
[2023-06-28 06:26:49,911] [INFO] Task started: Blastn
[2023-06-28 06:26:49,911] [INFO] Running command: blastn -query GCA_017416855.1_ASM1741685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02378f1f-856a-4da6-8bcc-c47356ffed1e/dqc_reference/reference_markers_gtdb.fasta -out GCA_017416855.1_ASM1741685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:26:50,923] [INFO] Task succeeded: Blastn
[2023-06-28 06:26:50,928] [INFO] Selected 12 target genomes.
[2023-06-28 06:26:50,929] [INFO] Target genome list was writen to GCA_017416855.1_ASM1741685v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:26:50,932] [INFO] Task started: fastANI
[2023-06-28 06:26:50,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg96bc1cda-edce-4103-ad9a-54776fd81bc8/GCA_017416855.1_ASM1741685v1_genomic.fna.gz --refList GCA_017416855.1_ASM1741685v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017416855.1_ASM1741685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:26:55,434] [INFO] Task succeeded: fastANI
[2023-06-28 06:26:55,444] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 06:26:55,445] [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_017416855.1	s__UMGS755 sp017416855	100.0	775	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015068865.1	s__UMGS755 sp015068865	86.8407	377	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068905.1	s__UMGS755 sp015068905	79.4258	170	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017407515.1	s__UMGS755 sp017407515	78.69	155	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017549205.1	s__UMGS755 sp017549205	78.5838	158	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017507525.1	s__UMGS755 sp017507525	78.4069	163	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545185.1	s__UMGS755 sp900545185	78.0998	100	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	99.96	99.96	0.89	0.89	2	-
GCA_015069045.1	s__UMGS755 sp015069045	77.6726	121	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068615.1	s__UMGS755 sp015068615	77.3369	101	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UMGS755	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 06:26:55,448] [INFO] GTDB search result was written to GCA_017416855.1_ASM1741685v1_genomic.fna/result_gtdb.tsv
[2023-06-28 06:26:55,448] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:26:55,451] [INFO] DFAST_QC result json was written to GCA_017416855.1_ASM1741685v1_genomic.fna/dqc_result.json
[2023-06-28 06:26:55,451] [INFO] DFAST_QC completed!
[2023-06-28 06:26:55,452] [INFO] Total running time: 0h0m50s