[2023-06-05 08:49:00,723] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:49:00,725] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:49:00,726] [INFO] DQC Reference Directory: /var/lib/cwl/stg92800c1a-a5eb-43d7-8e2a-2490b56f79c3/dqc_reference
[2023-06-05 08:49:02,486] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:49:02,487] [INFO] Task started: Prodigal
[2023-06-05 08:49:02,487] [INFO] Running command: gunzip -c /var/lib/cwl/stg15ee5497-4774-4b92-ae00-3c387c2206e7/GCA_934148445.1_ERR7738265_bin.40_genomic.fna.gz | prodigal -d GCA_934148445.1_ERR7738265_bin.40_genomic.fna/cds.fna -a GCA_934148445.1_ERR7738265_bin.40_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:49:04,826] [INFO] Task succeeded: Prodigal
[2023-06-05 08:49:04,826] [INFO] Task started: HMMsearch
[2023-06-05 08:49:04,826] [INFO] Running command: hmmsearch --tblout GCA_934148445.1_ERR7738265_bin.40_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92800c1a-a5eb-43d7-8e2a-2490b56f79c3/dqc_reference/reference_markers.hmm GCA_934148445.1_ERR7738265_bin.40_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:49:05,003] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:49:05,004] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg15ee5497-4774-4b92-ae00-3c387c2206e7/GCA_934148445.1_ERR7738265_bin.40_genomic.fna.gz]
[2023-06-05 08:49:05,019] [INFO] Query marker FASTA was written to GCA_934148445.1_ERR7738265_bin.40_genomic.fna/markers.fasta
[2023-06-05 08:49:05,019] [INFO] Task started: Blastn
[2023-06-05 08:49:05,019] [INFO] Running command: blastn -query GCA_934148445.1_ERR7738265_bin.40_genomic.fna/markers.fasta -db /var/lib/cwl/stg92800c1a-a5eb-43d7-8e2a-2490b56f79c3/dqc_reference/reference_markers.fasta -out GCA_934148445.1_ERR7738265_bin.40_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:49:06,098] [INFO] Task succeeded: Blastn
[2023-06-05 08:49:06,101] [INFO] Selected 20 target genomes.
[2023-06-05 08:49:06,101] [INFO] Target genome list was writen to GCA_934148445.1_ERR7738265_bin.40_genomic.fna/target_genomes.txt
[2023-06-05 08:49:06,107] [INFO] Task started: fastANI
[2023-06-05 08:49:06,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg15ee5497-4774-4b92-ae00-3c387c2206e7/GCA_934148445.1_ERR7738265_bin.40_genomic.fna.gz --refList GCA_934148445.1_ERR7738265_bin.40_genomic.fna/target_genomes.txt --output GCA_934148445.1_ERR7738265_bin.40_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:49:14,885] [INFO] Task succeeded: fastANI
[2023-06-05 08:49:14,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92800c1a-a5eb-43d7-8e2a-2490b56f79c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:49:14,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92800c1a-a5eb-43d7-8e2a-2490b56f79c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:49:14,892] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:49:14,892] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 08:49:14,893] [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
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	75.4549	63	489	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	75.102	51	489	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	75.0196	62	489	95	below_threshold
Romboutsia lituseburensis	strain=DSM 797	GCA_900103615.1	1537	1537	type	True	74.983	63	489	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	74.9423	63	489	95	below_threshold
[Clostridium] dakarense	strain=FF1	GCA_000499525.1	1301100	1301100	type	True	74.8487	66	489	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 08:49:14,894] [INFO] DFAST Taxonomy check result was written to GCA_934148445.1_ERR7738265_bin.40_genomic.fna/tc_result.tsv
[2023-06-05 08:49:14,895] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:49:14,895] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:49:14,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92800c1a-a5eb-43d7-8e2a-2490b56f79c3/dqc_reference/checkm_data
[2023-06-05 08:49:14,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:49:14,913] [INFO] Task started: CheckM
[2023-06-05 08:49:14,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934148445.1_ERR7738265_bin.40_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934148445.1_ERR7738265_bin.40_genomic.fna/checkm_input GCA_934148445.1_ERR7738265_bin.40_genomic.fna/checkm_result
[2023-06-05 08:49:28,110] [INFO] Task succeeded: CheckM
[2023-06-05 08:49:28,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:49:28,126] [INFO] ===== Completeness check finished =====
[2023-06-05 08:49:28,126] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:49:28,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934148445.1_ERR7738265_bin.40_genomic.fna/markers.fasta)
[2023-06-05 08:49:28,126] [INFO] Task started: Blastn
[2023-06-05 08:49:28,126] [INFO] Running command: blastn -query GCA_934148445.1_ERR7738265_bin.40_genomic.fna/markers.fasta -db /var/lib/cwl/stg92800c1a-a5eb-43d7-8e2a-2490b56f79c3/dqc_reference/reference_markers_gtdb.fasta -out GCA_934148445.1_ERR7738265_bin.40_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:49:28,804] [INFO] Task succeeded: Blastn
[2023-06-05 08:49:28,807] [INFO] Selected 6 target genomes.
[2023-06-05 08:49:28,807] [INFO] Target genome list was writen to GCA_934148445.1_ERR7738265_bin.40_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:49:28,836] [INFO] Task started: fastANI
[2023-06-05 08:49:28,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg15ee5497-4774-4b92-ae00-3c387c2206e7/GCA_934148445.1_ERR7738265_bin.40_genomic.fna.gz --refList GCA_934148445.1_ERR7738265_bin.40_genomic.fna/target_genomes_gtdb.txt --output GCA_934148445.1_ERR7738265_bin.40_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:49:31,014] [INFO] Task succeeded: fastANI
[2023-06-05 08:49:31,020] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 08:49:31,020] [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_000438255.1	s__CAG-269 sp000438255	98.6312	383	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.47	98.35	0.85	0.83	3	conclusive
GCA_900753165.1	s__CAG-269 sp900753165	87.1793	277	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.62	99.62	0.76	0.76	2	-
GCA_900552555.1	s__CAG-269 sp900552555	86.4135	352	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001916065.1	s__CAG-269 sp001916065	86.0901	343	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.24	97.60	0.86	0.82	5	-
GCA_900551615.1	s__CAG-269 sp900551615	85.9508	342	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.20	98.20	0.87	0.87	2	-
GCA_001916005.1	s__CAG-269 sp001916005	82.5014	296	489	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	96.70	96.22	0.72	0.66	3	-
--------------------------------------------------------------------------------
[2023-06-05 08:49:31,022] [INFO] GTDB search result was written to GCA_934148445.1_ERR7738265_bin.40_genomic.fna/result_gtdb.tsv
[2023-06-05 08:49:31,022] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:49:31,025] [INFO] DFAST_QC result json was written to GCA_934148445.1_ERR7738265_bin.40_genomic.fna/dqc_result.json
[2023-06-05 08:49:31,025] [INFO] DFAST_QC completed!
[2023-06-05 08:49:31,025] [INFO] Total running time: 0h0m30s