[2023-06-18 13:03:41,612] [INFO] DFAST_QC pipeline started.
[2023-06-18 13:03:41,616] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 13:03:41,616] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5ce5744-f16e-4e9b-ae32-2915bf075479/dqc_reference
[2023-06-18 13:03:42,823] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 13:03:42,824] [INFO] Task started: Prodigal
[2023-06-18 13:03:42,824] [INFO] Running command: gunzip -c /var/lib/cwl/stg73013f03-bf37-42c9-b320-5a34671c99b0/GCA_018402665.1_ASM1840266v1_genomic.fna.gz | prodigal -d GCA_018402665.1_ASM1840266v1_genomic.fna/cds.fna -a GCA_018402665.1_ASM1840266v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 13:03:52,357] [INFO] Task succeeded: Prodigal
[2023-06-18 13:03:52,357] [INFO] Task started: HMMsearch
[2023-06-18 13:03:52,358] [INFO] Running command: hmmsearch --tblout GCA_018402665.1_ASM1840266v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5ce5744-f16e-4e9b-ae32-2915bf075479/dqc_reference/reference_markers.hmm GCA_018402665.1_ASM1840266v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 13:03:52,572] [INFO] Task succeeded: HMMsearch
[2023-06-18 13:03:52,576] [INFO] Found 6/6 markers.
[2023-06-18 13:03:52,605] [INFO] Query marker FASTA was written to GCA_018402665.1_ASM1840266v1_genomic.fna/markers.fasta
[2023-06-18 13:03:52,606] [INFO] Task started: Blastn
[2023-06-18 13:03:52,606] [INFO] Running command: blastn -query GCA_018402665.1_ASM1840266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5ce5744-f16e-4e9b-ae32-2915bf075479/dqc_reference/reference_markers.fasta -out GCA_018402665.1_ASM1840266v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:03:53,213] [INFO] Task succeeded: Blastn
[2023-06-18 13:03:53,217] [INFO] Selected 30 target genomes.
[2023-06-18 13:03:53,218] [INFO] Target genome list was writen to GCA_018402665.1_ASM1840266v1_genomic.fna/target_genomes.txt
[2023-06-18 13:03:53,224] [INFO] Task started: fastANI
[2023-06-18 13:03:53,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg73013f03-bf37-42c9-b320-5a34671c99b0/GCA_018402665.1_ASM1840266v1_genomic.fna.gz --refList GCA_018402665.1_ASM1840266v1_genomic.fna/target_genomes.txt --output GCA_018402665.1_ASM1840266v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 13:04:09,533] [INFO] Task succeeded: fastANI
[2023-06-18 13:04:09,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5ce5744-f16e-4e9b-ae32-2915bf075479/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 13:04:09,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5ce5744-f16e-4e9b-ae32-2915bf075479/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 13:04:09,536] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 13:04:09,537] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 13:04:09,537] [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
--------------------------------------------------------------------------------
[2023-06-18 13:04:09,546] [INFO] DFAST Taxonomy check result was written to GCA_018402665.1_ASM1840266v1_genomic.fna/tc_result.tsv
[2023-06-18 13:04:09,546] [INFO] ===== Taxonomy check completed =====
[2023-06-18 13:04:09,547] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 13:04:09,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5ce5744-f16e-4e9b-ae32-2915bf075479/dqc_reference/checkm_data
[2023-06-18 13:04:09,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 13:04:09,581] [INFO] Task started: CheckM
[2023-06-18 13:04:09,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018402665.1_ASM1840266v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018402665.1_ASM1840266v1_genomic.fna/checkm_input GCA_018402665.1_ASM1840266v1_genomic.fna/checkm_result
[2023-06-18 13:04:41,901] [INFO] Task succeeded: CheckM
[2023-06-18 13:04:41,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 13:04:41,932] [INFO] ===== Completeness check finished =====
[2023-06-18 13:04:41,932] [INFO] ===== Start GTDB Search =====
[2023-06-18 13:04:41,932] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018402665.1_ASM1840266v1_genomic.fna/markers.fasta)
[2023-06-18 13:04:41,933] [INFO] Task started: Blastn
[2023-06-18 13:04:41,933] [INFO] Running command: blastn -query GCA_018402665.1_ASM1840266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5ce5744-f16e-4e9b-ae32-2915bf075479/dqc_reference/reference_markers_gtdb.fasta -out GCA_018402665.1_ASM1840266v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:04:42,711] [INFO] Task succeeded: Blastn
[2023-06-18 13:04:42,716] [INFO] Selected 15 target genomes.
[2023-06-18 13:04:42,717] [INFO] Target genome list was writen to GCA_018402665.1_ASM1840266v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 13:04:42,751] [INFO] Task started: fastANI
[2023-06-18 13:04:42,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg73013f03-bf37-42c9-b320-5a34671c99b0/GCA_018402665.1_ASM1840266v1_genomic.fna.gz --refList GCA_018402665.1_ASM1840266v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018402665.1_ASM1840266v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 13:04:49,036] [INFO] Task succeeded: fastANI
[2023-06-18 13:04:49,050] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 13:04:49,050] [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_018402665.1	s__UBA10364 sp018402665	100.0	633	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	96.42	96.42	0.92	0.92	2	conclusive
GCA_905478295.1	s__UBA10364 sp002387615	86.3613	504	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.55	99.11	0.94	0.89	10	-
GCA_002685435.1	s__UBA10364 sp002685435	84.3819	373	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003045825.1	s__UBA10364 sp003045825	83.9001	428	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.67	96.47	0.88	0.80	20	-
GCA_013911625.1	s__UBA10364 sp013911625	78.2358	76	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003455605.1	s__UBA10364 sp003455605	78.0482	82	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525035.1	s__UBA10364 sp011525035	77.8434	151	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003385605.1	s__UBA10364 sp003385605	77.8083	164	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.63	99.63	0.71	0.71	2	-
GCA_018623275.1	s__UBA10364 sp018623275	77.2406	97	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003545085.1	s__UBA10364 sp003545085	76.9932	88	636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 13:04:49,054] [INFO] GTDB search result was written to GCA_018402665.1_ASM1840266v1_genomic.fna/result_gtdb.tsv
[2023-06-18 13:04:49,055] [INFO] ===== GTDB Search completed =====
[2023-06-18 13:04:49,058] [INFO] DFAST_QC result json was written to GCA_018402665.1_ASM1840266v1_genomic.fna/dqc_result.json
[2023-06-18 13:04:49,059] [INFO] DFAST_QC completed!
[2023-06-18 13:04:49,059] [INFO] Total running time: 0h1m7s