[2023-06-28 23:05:46,756] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:05:46,758] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:05:46,759] [INFO] DQC Reference Directory: /var/lib/cwl/stg6106b033-a4c1-4520-9a4f-e0e6045a9652/dqc_reference
[2023-06-28 23:05:48,027] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:05:48,028] [INFO] Task started: Prodigal
[2023-06-28 23:05:48,028] [INFO] Running command: gunzip -c /var/lib/cwl/stgba392036-3863-4352-b96a-027e11f4fc90/GCA_027484485.1_ASM2748448v1_genomic.fna.gz | prodigal -d GCA_027484485.1_ASM2748448v1_genomic.fna/cds.fna -a GCA_027484485.1_ASM2748448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:05:59,024] [INFO] Task succeeded: Prodigal
[2023-06-28 23:05:59,024] [INFO] Task started: HMMsearch
[2023-06-28 23:05:59,024] [INFO] Running command: hmmsearch --tblout GCA_027484485.1_ASM2748448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6106b033-a4c1-4520-9a4f-e0e6045a9652/dqc_reference/reference_markers.hmm GCA_027484485.1_ASM2748448v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:05:59,192] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:05:59,194] [INFO] Found 6/6 markers.
[2023-06-28 23:05:59,215] [INFO] Query marker FASTA was written to GCA_027484485.1_ASM2748448v1_genomic.fna/markers.fasta
[2023-06-28 23:05:59,215] [INFO] Task started: Blastn
[2023-06-28 23:05:59,215] [INFO] Running command: blastn -query GCA_027484485.1_ASM2748448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6106b033-a4c1-4520-9a4f-e0e6045a9652/dqc_reference/reference_markers.fasta -out GCA_027484485.1_ASM2748448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:05:59,793] [INFO] Task succeeded: Blastn
[2023-06-28 23:05:59,797] [INFO] Selected 31 target genomes.
[2023-06-28 23:05:59,797] [INFO] Target genome list was writen to GCA_027484485.1_ASM2748448v1_genomic.fna/target_genomes.txt
[2023-06-28 23:05:59,844] [INFO] Task started: fastANI
[2023-06-28 23:05:59,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgba392036-3863-4352-b96a-027e11f4fc90/GCA_027484485.1_ASM2748448v1_genomic.fna.gz --refList GCA_027484485.1_ASM2748448v1_genomic.fna/target_genomes.txt --output GCA_027484485.1_ASM2748448v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:06:21,390] [INFO] Task succeeded: fastANI
[2023-06-28 23:06:21,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6106b033-a4c1-4520-9a4f-e0e6045a9652/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:06:21,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6106b033-a4c1-4520-9a4f-e0e6045a9652/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:06:21,392] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:06:21,392] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:06:21,392] [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 23:06:21,394] [INFO] DFAST Taxonomy check result was written to GCA_027484485.1_ASM2748448v1_genomic.fna/tc_result.tsv
[2023-06-28 23:06:21,395] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:06:21,395] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:06:21,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6106b033-a4c1-4520-9a4f-e0e6045a9652/dqc_reference/checkm_data
[2023-06-28 23:06:21,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:06:21,418] [INFO] Task started: CheckM
[2023-06-28 23:06:21,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027484485.1_ASM2748448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027484485.1_ASM2748448v1_genomic.fna/checkm_input GCA_027484485.1_ASM2748448v1_genomic.fna/checkm_result
[2023-06-28 23:06:54,706] [INFO] Task succeeded: CheckM
[2023-06-28 23:06:54,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 23:06:54,726] [INFO] ===== Completeness check finished =====
[2023-06-28 23:06:54,726] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:06:54,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027484485.1_ASM2748448v1_genomic.fna/markers.fasta)
[2023-06-28 23:06:54,726] [INFO] Task started: Blastn
[2023-06-28 23:06:54,726] [INFO] Running command: blastn -query GCA_027484485.1_ASM2748448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6106b033-a4c1-4520-9a4f-e0e6045a9652/dqc_reference/reference_markers_gtdb.fasta -out GCA_027484485.1_ASM2748448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:06:55,542] [INFO] Task succeeded: Blastn
[2023-06-28 23:06:55,546] [INFO] Selected 14 target genomes.
[2023-06-28 23:06:55,546] [INFO] Target genome list was writen to GCA_027484485.1_ASM2748448v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:06:55,575] [INFO] Task started: fastANI
[2023-06-28 23:06:55,575] [INFO] Running command: fastANI --query /var/lib/cwl/stgba392036-3863-4352-b96a-027e11f4fc90/GCA_027484485.1_ASM2748448v1_genomic.fna.gz --refList GCA_027484485.1_ASM2748448v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027484485.1_ASM2748448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:07:01,562] [INFO] Task succeeded: fastANI
[2023-06-28 23:07:01,570] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:07:01,570] [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_016868755.1	s__TMED14 sp016868755	82.4661	397	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005786915.1	s__TMED14 sp005786915	81.9219	299	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903821715.1	s__TMED14 sp903821715	81.1275	321	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003451355.1	s__TMED14 sp003451355	81.1247	263	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292855.1	s__TMED14 sp002292855	78.8242	280	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205365.1	s__TMED14 sp013205365	78.7502	202	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737315.1	s__TMED14 sp002737315	78.7174	221	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	99.85	99.85	0.92	0.92	2	-
GCA_002381225.1	s__TMED14 sp002381225	76.551	65	584	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	98.92	98.57	0.92	0.89	11	-
--------------------------------------------------------------------------------
[2023-06-28 23:07:01,572] [INFO] GTDB search result was written to GCA_027484485.1_ASM2748448v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:07:01,573] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:07:01,576] [INFO] DFAST_QC result json was written to GCA_027484485.1_ASM2748448v1_genomic.fna/dqc_result.json
[2023-06-28 23:07:01,576] [INFO] DFAST_QC completed!
[2023-06-28 23:07:01,576] [INFO] Total running time: 0h1m15s