[2023-06-04 23:57:36,080] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:57:36,084] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:57:36,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg05e22b9d-4af7-4952-955d-f20426aea665/dqc_reference
[2023-06-04 23:57:38,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:57:38,138] [INFO] Task started: Prodigal
[2023-06-04 23:57:38,138] [INFO] Running command: gunzip -c /var/lib/cwl/stgfae35e07-a0c3-4fab-a7f6-60126fe990e5/GCA_934339045.1_ERR7738544_bin.198_genomic.fna.gz | prodigal -d GCA_934339045.1_ERR7738544_bin.198_genomic.fna/cds.fna -a GCA_934339045.1_ERR7738544_bin.198_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:57:44,626] [INFO] Task succeeded: Prodigal
[2023-06-04 23:57:44,626] [INFO] Task started: HMMsearch
[2023-06-04 23:57:44,626] [INFO] Running command: hmmsearch --tblout GCA_934339045.1_ERR7738544_bin.198_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05e22b9d-4af7-4952-955d-f20426aea665/dqc_reference/reference_markers.hmm GCA_934339045.1_ERR7738544_bin.198_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:57:44,908] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:57:44,910] [INFO] Found 6/6 markers.
[2023-06-04 23:57:44,950] [INFO] Query marker FASTA was written to GCA_934339045.1_ERR7738544_bin.198_genomic.fna/markers.fasta
[2023-06-04 23:57:44,951] [INFO] Task started: Blastn
[2023-06-04 23:57:44,951] [INFO] Running command: blastn -query GCA_934339045.1_ERR7738544_bin.198_genomic.fna/markers.fasta -db /var/lib/cwl/stg05e22b9d-4af7-4952-955d-f20426aea665/dqc_reference/reference_markers.fasta -out GCA_934339045.1_ERR7738544_bin.198_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:57:45,587] [INFO] Task succeeded: Blastn
[2023-06-04 23:57:45,592] [INFO] Selected 25 target genomes.
[2023-06-04 23:57:45,593] [INFO] Target genome list was writen to GCA_934339045.1_ERR7738544_bin.198_genomic.fna/target_genomes.txt
[2023-06-04 23:57:45,595] [INFO] Task started: fastANI
[2023-06-04 23:57:45,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgfae35e07-a0c3-4fab-a7f6-60126fe990e5/GCA_934339045.1_ERR7738544_bin.198_genomic.fna.gz --refList GCA_934339045.1_ERR7738544_bin.198_genomic.fna/target_genomes.txt --output GCA_934339045.1_ERR7738544_bin.198_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:57:58,486] [INFO] Task succeeded: fastANI
[2023-06-04 23:57:58,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05e22b9d-4af7-4952-955d-f20426aea665/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:57:58,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05e22b9d-4af7-4952-955d-f20426aea665/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:57:58,497] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:57:58,497] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 23:57:58,498] [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
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	80.6659	299	993	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	80.5528	302	993	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	77.8815	53	993	95	below_threshold
Eubacterium uniforme	strain=ATCC 35992	GCA_900167115.1	39495	39495	type	True	77.6911	78	993	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	77.4904	50	993	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	76.5836	58	993	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 23:57:58,500] [INFO] DFAST Taxonomy check result was written to GCA_934339045.1_ERR7738544_bin.198_genomic.fna/tc_result.tsv
[2023-06-04 23:57:58,500] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:57:58,500] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:57:58,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05e22b9d-4af7-4952-955d-f20426aea665/dqc_reference/checkm_data
[2023-06-04 23:57:58,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:57:58,539] [INFO] Task started: CheckM
[2023-06-04 23:57:58,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934339045.1_ERR7738544_bin.198_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934339045.1_ERR7738544_bin.198_genomic.fna/checkm_input GCA_934339045.1_ERR7738544_bin.198_genomic.fna/checkm_result
[2023-06-04 23:58:24,203] [INFO] Task succeeded: CheckM
[2023-06-04 23:58:24,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:58:24,226] [INFO] ===== Completeness check finished =====
[2023-06-04 23:58:24,226] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:58:24,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934339045.1_ERR7738544_bin.198_genomic.fna/markers.fasta)
[2023-06-04 23:58:24,227] [INFO] Task started: Blastn
[2023-06-04 23:58:24,227] [INFO] Running command: blastn -query GCA_934339045.1_ERR7738544_bin.198_genomic.fna/markers.fasta -db /var/lib/cwl/stg05e22b9d-4af7-4952-955d-f20426aea665/dqc_reference/reference_markers_gtdb.fasta -out GCA_934339045.1_ERR7738544_bin.198_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:58:25,256] [INFO] Task succeeded: Blastn
[2023-06-04 23:58:25,261] [INFO] Selected 12 target genomes.
[2023-06-04 23:58:25,261] [INFO] Target genome list was writen to GCA_934339045.1_ERR7738544_bin.198_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:58:25,263] [INFO] Task started: fastANI
[2023-06-04 23:58:25,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgfae35e07-a0c3-4fab-a7f6-60126fe990e5/GCA_934339045.1_ERR7738544_bin.198_genomic.fna.gz --refList GCA_934339045.1_ERR7738544_bin.198_genomic.fna/target_genomes_gtdb.txt --output GCA_934339045.1_ERR7738544_bin.198_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:58:30,454] [INFO] Task succeeded: fastANI
[2023-06-04 23:58:30,467] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 23:58:30,467] [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_900548465.1	s__Eubacterium_G sp900548465	97.4869	598	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	97.75	97.64	0.80	0.72	3	conclusive
GCF_000153885.1	s__Eubacterium_G ventriosum	80.5528	302	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	97.67	0.81	0.64	20	-
GCA_900764695.1	s__Eubacterium_G sp900764695	80.2389	214	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003460505.1	s__Eubacterium_G sp000435815	80.2118	311	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.79	97.65	0.84	0.54	8	-
GCA_900550135.1	s__Eubacterium_G sp900550135	80.1248	272	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.87	97.32	0.76	0.74	4	-
GCA_902363805.1	s__Eubacterium_G sp000434315	79.8027	225	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	98.14	0.87	0.84	6	-
GCF_003479405.1	s__Eubacterium_G sp000432355	79.537	306	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	99.22	97.56	0.94	0.86	9	-
GCA_910578975.1	s__Eubacterium_G sp910578975	78.8848	245	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584795.1	s__Eubacterium_G sp910584795	78.8158	224	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574895.1	s__Eubacterium_G sp910574895	78.6143	246	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420085.1	s__Eubacterium_G sp904420085	77.8608	182	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766735.1	s__Eubacterium_G sp902766735	77.2481	136	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 23:58:30,469] [INFO] GTDB search result was written to GCA_934339045.1_ERR7738544_bin.198_genomic.fna/result_gtdb.tsv
[2023-06-04 23:58:30,470] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:58:30,473] [INFO] DFAST_QC result json was written to GCA_934339045.1_ERR7738544_bin.198_genomic.fna/dqc_result.json
[2023-06-04 23:58:30,473] [INFO] DFAST_QC completed!
[2023-06-04 23:58:30,473] [INFO] Total running time: 0h0m54s