[2023-06-05 04:33:52,603] [INFO] DFAST_QC pipeline started.
[2023-06-05 04:33:52,605] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 04:33:52,605] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a9152c3-9d9a-4776-9d63-7f5bd2637ea9/dqc_reference
[2023-06-05 04:33:54,407] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 04:33:54,408] [INFO] Task started: Prodigal
[2023-06-05 04:33:54,408] [INFO] Running command: gunzip -c /var/lib/cwl/stg37be5b0f-2bf8-4fa0-947b-411a80939c05/GCA_934840365.1_MTG227_bin.20.fa_genomic.fna.gz | prodigal -d GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/cds.fna -a GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:34:00,311] [INFO] Task succeeded: Prodigal
[2023-06-05 04:34:00,312] [INFO] Task started: HMMsearch
[2023-06-05 04:34:00,312] [INFO] Running command: hmmsearch --tblout GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a9152c3-9d9a-4776-9d63-7f5bd2637ea9/dqc_reference/reference_markers.hmm GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:34:00,475] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:34:00,476] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg37be5b0f-2bf8-4fa0-947b-411a80939c05/GCA_934840365.1_MTG227_bin.20.fa_genomic.fna.gz]
[2023-06-05 04:34:00,496] [INFO] Query marker FASTA was written to GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/markers.fasta
[2023-06-05 04:34:00,496] [INFO] Task started: Blastn
[2023-06-05 04:34:00,496] [INFO] Running command: blastn -query GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a9152c3-9d9a-4776-9d63-7f5bd2637ea9/dqc_reference/reference_markers.fasta -out GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:34:01,079] [INFO] Task succeeded: Blastn
[2023-06-05 04:34:01,082] [INFO] Selected 6 target genomes.
[2023-06-05 04:34:01,082] [INFO] Target genome list was writen to GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/target_genomes.txt
[2023-06-05 04:34:01,085] [INFO] Task started: fastANI
[2023-06-05 04:34:01,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg37be5b0f-2bf8-4fa0-947b-411a80939c05/GCA_934840365.1_MTG227_bin.20.fa_genomic.fna.gz --refList GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/target_genomes.txt --output GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:34:04,658] [INFO] Task succeeded: fastANI
[2023-06-05 04:34:04,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a9152c3-9d9a-4776-9d63-7f5bd2637ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:34:04,659] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a9152c3-9d9a-4776-9d63-7f5bd2637ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:34:04,666] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:34:04,666] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 04:34:04,666] [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	85.9077	440	548	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	83.9405	414	548	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	83.9103	404	548	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	83.5095	410	548	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	80.2835	278	548	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	78.0414	126	548	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 04:34:04,668] [INFO] DFAST Taxonomy check result was written to GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/tc_result.tsv
[2023-06-05 04:34:04,669] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:34:04,669] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:34:04,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a9152c3-9d9a-4776-9d63-7f5bd2637ea9/dqc_reference/checkm_data
[2023-06-05 04:34:04,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:34:04,691] [INFO] Task started: CheckM
[2023-06-05 04:34:04,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/checkm_input GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/checkm_result
[2023-06-05 04:34:28,091] [INFO] Task succeeded: CheckM
[2023-06-05 04:34:28,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.97%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 04:34:28,111] [INFO] ===== Completeness check finished =====
[2023-06-05 04:34:28,111] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:34:28,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/markers.fasta)
[2023-06-05 04:34:28,111] [INFO] Task started: Blastn
[2023-06-05 04:34:28,112] [INFO] Running command: blastn -query GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a9152c3-9d9a-4776-9d63-7f5bd2637ea9/dqc_reference/reference_markers_gtdb.fasta -out GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:34:28,893] [INFO] Task succeeded: Blastn
[2023-06-05 04:34:28,897] [INFO] Selected 11 target genomes.
[2023-06-05 04:34:28,897] [INFO] Target genome list was writen to GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:34:28,906] [INFO] Task started: fastANI
[2023-06-05 04:34:28,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg37be5b0f-2bf8-4fa0-947b-411a80939c05/GCA_934840365.1_MTG227_bin.20.fa_genomic.fna.gz --refList GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:34:34,712] [INFO] Task succeeded: fastANI
[2023-06-05 04:34:34,721] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 04:34:34,722] [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
GCF_002549755.1	s__Faecalibacterium prausnitzii_D	97.4383	504	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.37	96.64	0.86	0.78	38	conclusive
GCA_900539885.1	s__Faecalibacterium sp900539885	92.1301	471	548	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_002549775.1	s__Faecalibacterium prausnitzii_F	88.0904	476	548	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	86.1611	428	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.71	98.00	0.92	0.86	4	-
GCF_003324185.1	s__Faecalibacterium prausnitzii	85.9077	440	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.64	96.12	0.86	0.79	47	-
GCF_003287405.1	s__Faecalibacterium prausnitzii_J	85.8238	434	548	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_905215595.1	s__Faecalibacterium sp905215595	85.7739	357	548	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_002550015.1	s__Faecalibacterium prausnitzii_A	85.6244	446	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.42	95.34	0.88	0.83	7	-
GCA_003449675.1	s__Faecalibacterium sp003449675	85.4927	328	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	96.56	96.55	0.80	0.74	3	-
GCA_900772565.1	s__Faecalibacterium sp900772565	85.3866	415	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 04:34:34,723] [INFO] GTDB search result was written to GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 04:34:34,724] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:34:34,727] [INFO] DFAST_QC result json was written to GCA_934840365.1_MTG227_bin.20.fa_genomic.fna/dqc_result.json
[2023-06-05 04:34:34,728] [INFO] DFAST_QC completed!
[2023-06-05 04:34:34,728] [INFO] Total running time: 0h0m42s