[2023-06-13 15:57:47,184] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:57:47,186] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:57:47,186] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e530a58-7aa3-4efd-b341-9241af1ec0de/dqc_reference
[2023-06-13 15:57:48,315] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:57:48,316] [INFO] Task started: Prodigal
[2023-06-13 15:57:48,316] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf858563-f560-40ad-8763-8a3942e024ba/GCA_022749395.1_ASM2274939v1_genomic.fna.gz | prodigal -d GCA_022749395.1_ASM2274939v1_genomic.fna/cds.fna -a GCA_022749395.1_ASM2274939v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:57:54,457] [INFO] Task succeeded: Prodigal
[2023-06-13 15:57:54,457] [INFO] Task started: HMMsearch
[2023-06-13 15:57:54,457] [INFO] Running command: hmmsearch --tblout GCA_022749395.1_ASM2274939v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e530a58-7aa3-4efd-b341-9241af1ec0de/dqc_reference/reference_markers.hmm GCA_022749395.1_ASM2274939v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:57:54,648] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:57:54,649] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdf858563-f560-40ad-8763-8a3942e024ba/GCA_022749395.1_ASM2274939v1_genomic.fna.gz]
[2023-06-13 15:57:54,683] [INFO] Query marker FASTA was written to GCA_022749395.1_ASM2274939v1_genomic.fna/markers.fasta
[2023-06-13 15:57:54,683] [INFO] Task started: Blastn
[2023-06-13 15:57:54,683] [INFO] Running command: blastn -query GCA_022749395.1_ASM2274939v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e530a58-7aa3-4efd-b341-9241af1ec0de/dqc_reference/reference_markers.fasta -out GCA_022749395.1_ASM2274939v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:57:55,349] [INFO] Task succeeded: Blastn
[2023-06-13 15:57:55,354] [INFO] Selected 7 target genomes.
[2023-06-13 15:57:55,354] [INFO] Target genome list was writen to GCA_022749395.1_ASM2274939v1_genomic.fna/target_genomes.txt
[2023-06-13 15:57:55,355] [INFO] Task started: fastANI
[2023-06-13 15:57:55,355] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf858563-f560-40ad-8763-8a3942e024ba/GCA_022749395.1_ASM2274939v1_genomic.fna.gz --refList GCA_022749395.1_ASM2274939v1_genomic.fna/target_genomes.txt --output GCA_022749395.1_ASM2274939v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:57:59,203] [INFO] Task succeeded: fastANI
[2023-06-13 15:57:59,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e530a58-7aa3-4efd-b341-9241af1ec0de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:57:59,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e530a58-7aa3-4efd-b341-9241af1ec0de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:57:59,212] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:57:59,212] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:57:59,212] [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
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	94.3883	454	512	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	83.3065	382	512	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	83.2473	382	512	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	83.1338	372	512	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	79.9292	251	512	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	78.1024	141	512	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	77.9586	120	512	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:57:59,214] [INFO] DFAST Taxonomy check result was written to GCA_022749395.1_ASM2274939v1_genomic.fna/tc_result.tsv
[2023-06-13 15:57:59,215] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:57:59,215] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:57:59,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e530a58-7aa3-4efd-b341-9241af1ec0de/dqc_reference/checkm_data
[2023-06-13 15:57:59,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:57:59,243] [INFO] Task started: CheckM
[2023-06-13 15:57:59,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022749395.1_ASM2274939v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022749395.1_ASM2274939v1_genomic.fna/checkm_input GCA_022749395.1_ASM2274939v1_genomic.fna/checkm_result
[2023-06-13 15:58:22,935] [INFO] Task succeeded: CheckM
[2023-06-13 15:58:22,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.25%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 15:58:22,956] [INFO] ===== Completeness check finished =====
[2023-06-13 15:58:22,957] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:58:22,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022749395.1_ASM2274939v1_genomic.fna/markers.fasta)
[2023-06-13 15:58:22,957] [INFO] Task started: Blastn
[2023-06-13 15:58:22,957] [INFO] Running command: blastn -query GCA_022749395.1_ASM2274939v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e530a58-7aa3-4efd-b341-9241af1ec0de/dqc_reference/reference_markers_gtdb.fasta -out GCA_022749395.1_ASM2274939v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:58:24,055] [INFO] Task succeeded: Blastn
[2023-06-13 15:58:24,058] [INFO] Selected 11 target genomes.
[2023-06-13 15:58:24,058] [INFO] Target genome list was writen to GCA_022749395.1_ASM2274939v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:58:24,060] [INFO] Task started: fastANI
[2023-06-13 15:58:24,060] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf858563-f560-40ad-8763-8a3942e024ba/GCA_022749395.1_ASM2274939v1_genomic.fna.gz --refList GCA_022749395.1_ASM2274939v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022749395.1_ASM2274939v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:58:29,716] [INFO] Task succeeded: fastANI
[2023-06-13 15:58:29,726] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:58:29,726] [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_003449675.1	s__Faecalibacterium sp003449675	96.0097	342	512	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	96.56	96.55	0.80	0.74	3	conclusive
GCF_002550015.1	s__Faecalibacterium prausnitzii_A	94.5713	455	512	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.42	95.34	0.88	0.83	7	-
GCF_003324185.1	s__Faecalibacterium prausnitzii	94.3883	454	512	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.64	96.12	0.86	0.79	47	-
GCA_905215595.1	s__Faecalibacterium sp905215595	94.0659	369	512	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287405.1	s__Faecalibacterium prausnitzii_J	94.0453	449	512	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.32	96.98	0.87	0.83	5	-
GCA_900772565.1	s__Faecalibacterium sp900772565	93.7896	416	512	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002549775.1	s__Faecalibacterium prausnitzii_F	85.5568	395	512	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.99	97.71	0.95	0.94	3	-
GCA_900539945.1	s__Faecalibacterium sp900539945	85.4184	386	512	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.71	98.00	0.92	0.86	4	-
GCA_900539885.1	s__Faecalibacterium sp900539885	85.3557	382	512	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.54	97.23	0.89	0.84	6	-
GCF_002549755.1	s__Faecalibacterium prausnitzii_D	85.2761	399	512	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.37	96.64	0.86	0.78	38	-
GCA_900765105.1	s__Faecalibacterium sp900765105	84.772	327	512	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.27	98.27	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-13 15:58:29,728] [INFO] GTDB search result was written to GCA_022749395.1_ASM2274939v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:58:29,729] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:58:29,732] [INFO] DFAST_QC result json was written to GCA_022749395.1_ASM2274939v1_genomic.fna/dqc_result.json
[2023-06-13 15:58:29,732] [INFO] DFAST_QC completed!
[2023-06-13 15:58:29,732] [INFO] Total running time: 0h0m43s