[2023-06-18 22:25:27,023] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:25:27,026] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:25:27,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg022208b7-9a1c-4966-a15e-29da233f2696/dqc_reference
[2023-06-18 22:25:30,080] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:25:30,082] [INFO] Task started: Prodigal
[2023-06-18 22:25:30,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg43f36416-1d40-44f7-be59-e59637dfab72/GCA_013289925.1_ASM1328992v1_genomic.fna.gz | prodigal -d GCA_013289925.1_ASM1328992v1_genomic.fna/cds.fna -a GCA_013289925.1_ASM1328992v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:25:42,082] [INFO] Task succeeded: Prodigal
[2023-06-18 22:25:42,083] [INFO] Task started: HMMsearch
[2023-06-18 22:25:42,083] [INFO] Running command: hmmsearch --tblout GCA_013289925.1_ASM1328992v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg022208b7-9a1c-4966-a15e-29da233f2696/dqc_reference/reference_markers.hmm GCA_013289925.1_ASM1328992v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:25:42,335] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:25:42,336] [INFO] Found 6/6 markers.
[2023-06-18 22:25:42,380] [INFO] Query marker FASTA was written to GCA_013289925.1_ASM1328992v1_genomic.fna/markers.fasta
[2023-06-18 22:25:42,381] [INFO] Task started: Blastn
[2023-06-18 22:25:42,381] [INFO] Running command: blastn -query GCA_013289925.1_ASM1328992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg022208b7-9a1c-4966-a15e-29da233f2696/dqc_reference/reference_markers.fasta -out GCA_013289925.1_ASM1328992v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:25:42,980] [INFO] Task succeeded: Blastn
[2023-06-18 22:25:42,989] [INFO] Selected 23 target genomes.
[2023-06-18 22:25:42,989] [INFO] Target genome list was writen to GCA_013289925.1_ASM1328992v1_genomic.fna/target_genomes.txt
[2023-06-18 22:25:42,992] [INFO] Task started: fastANI
[2023-06-18 22:25:42,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg43f36416-1d40-44f7-be59-e59637dfab72/GCA_013289925.1_ASM1328992v1_genomic.fna.gz --refList GCA_013289925.1_ASM1328992v1_genomic.fna/target_genomes.txt --output GCA_013289925.1_ASM1328992v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:26:01,735] [INFO] Task succeeded: fastANI
[2023-06-18 22:26:01,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg022208b7-9a1c-4966-a15e-29da233f2696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:26:01,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg022208b7-9a1c-4966-a15e-29da233f2696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:26:01,743] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:26:01,744] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 22:26:01,744] [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
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	76.2331	61	1331	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	76.1284	61	1331	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.108	58	1331	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	76.108	58	1331	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	75.8834	64	1331	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 22:26:01,748] [INFO] DFAST Taxonomy check result was written to GCA_013289925.1_ASM1328992v1_genomic.fna/tc_result.tsv
[2023-06-18 22:26:01,748] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:26:01,748] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:26:01,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg022208b7-9a1c-4966-a15e-29da233f2696/dqc_reference/checkm_data
[2023-06-18 22:26:01,750] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:26:01,794] [INFO] Task started: CheckM
[2023-06-18 22:26:01,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013289925.1_ASM1328992v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013289925.1_ASM1328992v1_genomic.fna/checkm_input GCA_013289925.1_ASM1328992v1_genomic.fna/checkm_result
[2023-06-18 22:26:39,724] [INFO] Task succeeded: CheckM
[2023-06-18 22:26:39,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 22:26:39,752] [INFO] ===== Completeness check finished =====
[2023-06-18 22:26:39,752] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:26:39,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013289925.1_ASM1328992v1_genomic.fna/markers.fasta)
[2023-06-18 22:26:39,753] [INFO] Task started: Blastn
[2023-06-18 22:26:39,753] [INFO] Running command: blastn -query GCA_013289925.1_ASM1328992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg022208b7-9a1c-4966-a15e-29da233f2696/dqc_reference/reference_markers_gtdb.fasta -out GCA_013289925.1_ASM1328992v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:26:40,562] [INFO] Task succeeded: Blastn
[2023-06-18 22:26:40,568] [INFO] Selected 21 target genomes.
[2023-06-18 22:26:40,569] [INFO] Target genome list was writen to GCA_013289925.1_ASM1328992v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:26:40,575] [INFO] Task started: fastANI
[2023-06-18 22:26:40,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg43f36416-1d40-44f7-be59-e59637dfab72/GCA_013289925.1_ASM1328992v1_genomic.fna.gz --refList GCA_013289925.1_ASM1328992v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013289925.1_ASM1328992v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:26:57,149] [INFO] Task succeeded: fastANI
[2023-06-18 22:26:57,165] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:26:57,165] [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_003225465.1	s__Gp1-AA133 sp003225465	95.4394	1038	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Gp1-AA133	95.0	97.18	95.46	0.82	0.78	3	conclusive
GCA_003224995.1	s__Gp1-AA133 sp003224995	78.9603	348	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Gp1-AA133	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289685.1	s__Sulfotelmatobacter sp013289685	77.0301	215	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883425.1	s__Sulfotelmatobacter sp017883425	76.976	163	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290255.1	s__Sulfotelmatobacter kueseliae	76.9276	202	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883385.1	s__Sulfotelmatobacter sp017883385	76.7968	201	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003225555.1	s__Sulfotelmatobacter sp003225555	76.7921	140	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136335.1	s__Sulfotelmatobacter sp003136335	76.6774	121	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268755.1	s__KAN-5 sp018268755	76.6498	176	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__KAN-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003224905.1	s__QIAA01 sp003224905	76.6265	123	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__QIAA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003131585.1	s__Sulfotelmatobacter sp003131585	76.5788	188	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	99.89	99.89	0.95	0.95	2	-
GCA_003134995.1	s__Sulfotelmatobacter sp003134995	76.5558	180	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	99.91	99.75	0.99	0.98	6	-
GCA_003225595.1	s__Gp1-AA124 sp003225595	76.5379	145	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Gp1-AA124	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003168355.1	s__Sulfotelmatobacter sp003168355	76.4927	173	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	99.78	99.75	0.93	0.92	6	-
GCA_013289795.1	s__JABCZH01 sp013289795	76.4728	149	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__JABCZH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019244045.1	s__Gp1-AA122 sp019244045	76.3897	90	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Gp1-AA122	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003168235.1	s__Bog-209 sp003168235	76.2664	78	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	98.61	98.61	0.71	0.71	2	-
GCA_003164855.1	s__Sulfotelmatobacter sp003164855	76.2276	146	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132825.1	s__PALSA-270 sp003132825	76.2233	133	1331	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__PALSA-270	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 22:26:57,168] [INFO] GTDB search result was written to GCA_013289925.1_ASM1328992v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:26:57,171] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:26:57,175] [INFO] DFAST_QC result json was written to GCA_013289925.1_ASM1328992v1_genomic.fna/dqc_result.json
[2023-06-18 22:26:57,176] [INFO] DFAST_QC completed!
[2023-06-18 22:26:57,176] [INFO] Total running time: 0h1m30s