[2023-06-19 02:25:10,971] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:25:10,973] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:25:10,973] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f6da5eb-9df5-4b7e-9091-1d2b76f4cd07/dqc_reference
[2023-06-19 02:25:12,146] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:25:12,146] [INFO] Task started: Prodigal
[2023-06-19 02:25:12,147] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c22a65d-4c74-4e8e-bb25-f94a988e9599/GCA_018402585.1_ASM1840258v1_genomic.fna.gz | prodigal -d GCA_018402585.1_ASM1840258v1_genomic.fna/cds.fna -a GCA_018402585.1_ASM1840258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:25:28,824] [INFO] Task succeeded: Prodigal
[2023-06-19 02:25:28,824] [INFO] Task started: HMMsearch
[2023-06-19 02:25:28,825] [INFO] Running command: hmmsearch --tblout GCA_018402585.1_ASM1840258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f6da5eb-9df5-4b7e-9091-1d2b76f4cd07/dqc_reference/reference_markers.hmm GCA_018402585.1_ASM1840258v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:25:29,074] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:25:29,076] [INFO] Found 6/6 markers.
[2023-06-19 02:25:29,114] [INFO] Query marker FASTA was written to GCA_018402585.1_ASM1840258v1_genomic.fna/markers.fasta
[2023-06-19 02:25:29,115] [INFO] Task started: Blastn
[2023-06-19 02:25:29,115] [INFO] Running command: blastn -query GCA_018402585.1_ASM1840258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f6da5eb-9df5-4b7e-9091-1d2b76f4cd07/dqc_reference/reference_markers.fasta -out GCA_018402585.1_ASM1840258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:25:29,759] [INFO] Task succeeded: Blastn
[2023-06-19 02:25:29,763] [INFO] Selected 15 target genomes.
[2023-06-19 02:25:29,764] [INFO] Target genome list was writen to GCA_018402585.1_ASM1840258v1_genomic.fna/target_genomes.txt
[2023-06-19 02:25:29,767] [INFO] Task started: fastANI
[2023-06-19 02:25:29,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c22a65d-4c74-4e8e-bb25-f94a988e9599/GCA_018402585.1_ASM1840258v1_genomic.fna.gz --refList GCA_018402585.1_ASM1840258v1_genomic.fna/target_genomes.txt --output GCA_018402585.1_ASM1840258v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:25:42,806] [INFO] Task succeeded: fastANI
[2023-06-19 02:25:42,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f6da5eb-9df5-4b7e-9091-1d2b76f4cd07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:25:42,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f6da5eb-9df5-4b7e-9091-1d2b76f4cd07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:25:42,816] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:25:42,817] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 02:25:42,817] [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
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	76.5287	64	803	95	below_threshold
Terrimicrobium sacchariphilum	strain=NM-5	GCA_001613545.1	690879	690879	type	True	76.4237	62	803	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	76.209	63	803	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 02:25:42,848] [INFO] DFAST Taxonomy check result was written to GCA_018402585.1_ASM1840258v1_genomic.fna/tc_result.tsv
[2023-06-19 02:25:42,849] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:25:42,849] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:25:42,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f6da5eb-9df5-4b7e-9091-1d2b76f4cd07/dqc_reference/checkm_data
[2023-06-19 02:25:42,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:25:42,880] [INFO] Task started: CheckM
[2023-06-19 02:25:42,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018402585.1_ASM1840258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018402585.1_ASM1840258v1_genomic.fna/checkm_input GCA_018402585.1_ASM1840258v1_genomic.fna/checkm_result
[2023-06-19 02:26:30,806] [INFO] Task succeeded: CheckM
[2023-06-19 02:26:30,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:26:30,828] [INFO] ===== Completeness check finished =====
[2023-06-19 02:26:30,828] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:26:30,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018402585.1_ASM1840258v1_genomic.fna/markers.fasta)
[2023-06-19 02:26:30,829] [INFO] Task started: Blastn
[2023-06-19 02:26:30,829] [INFO] Running command: blastn -query GCA_018402585.1_ASM1840258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f6da5eb-9df5-4b7e-9091-1d2b76f4cd07/dqc_reference/reference_markers_gtdb.fasta -out GCA_018402585.1_ASM1840258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:26:31,657] [INFO] Task succeeded: Blastn
[2023-06-19 02:26:31,661] [INFO] Selected 10 target genomes.
[2023-06-19 02:26:31,662] [INFO] Target genome list was writen to GCA_018402585.1_ASM1840258v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:26:31,666] [INFO] Task started: fastANI
[2023-06-19 02:26:31,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c22a65d-4c74-4e8e-bb25-f94a988e9599/GCA_018402585.1_ASM1840258v1_genomic.fna.gz --refList GCA_018402585.1_ASM1840258v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018402585.1_ASM1840258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:26:38,721] [INFO] Task succeeded: fastANI
[2023-06-19 02:26:38,732] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:26:38,732] [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_018402585.1	s__JACTMZ01 sp018402585	100.0	802	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JACTMZ01;g__JACTMZ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903934135.1	s__JACTMZ01 sp903934135	86.8802	499	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JACTMZ01;g__JACTMZ01	95.0	99.34	99.34	0.86	0.86	2	-
GCA_903953565.1	s__JACTMZ01 sp903953565	80.383	428	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JACTMZ01;g__JACTMZ01	95.0	99.90	99.90	0.96	0.96	2	-
GCA_017853515.1	s__JACTMZ01 sp017853515	79.2769	266	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JACTMZ01;g__JACTMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883245.1	s__JACTMZ01 sp018883245	78.4424	259	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JACTMZ01;g__JACTMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879535.1	s__JACTMZ01 sp014879535	78.2018	265	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JACTMZ01;g__JACTMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402345.1	s__UBA967 sp018402345	77.1845	70	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 02:26:38,734] [INFO] GTDB search result was written to GCA_018402585.1_ASM1840258v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:26:38,735] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:26:38,738] [INFO] DFAST_QC result json was written to GCA_018402585.1_ASM1840258v1_genomic.fna/dqc_result.json
[2023-06-19 02:26:38,738] [INFO] DFAST_QC completed!
[2023-06-19 02:26:38,738] [INFO] Total running time: 0h1m28s