[2024-01-24 13:41:40,744] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,745] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,746] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d5f1803-ba20-441a-9458-9e1dc558b956/dqc_reference
[2024-01-24 13:41:42,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,123] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,124] [INFO] Running command: gunzip -c /var/lib/cwl/stg542389af-036a-4091-9baf-0d73b66c36f6/GCF_014287615.1_ASM1428761v1_genomic.fna.gz | prodigal -d GCF_014287615.1_ASM1428761v1_genomic.fna/cds.fna -a GCF_014287615.1_ASM1428761v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:58,702] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:58,702] [INFO] Task started: HMMsearch
[2024-01-24 13:41:58,702] [INFO] Running command: hmmsearch --tblout GCF_014287615.1_ASM1428761v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d5f1803-ba20-441a-9458-9e1dc558b956/dqc_reference/reference_markers.hmm GCF_014287615.1_ASM1428761v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:59,052] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:59,054] [INFO] Found 6/6 markers.
[2024-01-24 13:41:59,114] [INFO] Query marker FASTA was written to GCF_014287615.1_ASM1428761v1_genomic.fna/markers.fasta
[2024-01-24 13:41:59,115] [INFO] Task started: Blastn
[2024-01-24 13:41:59,115] [INFO] Running command: blastn -query GCF_014287615.1_ASM1428761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d5f1803-ba20-441a-9458-9e1dc558b956/dqc_reference/reference_markers.fasta -out GCF_014287615.1_ASM1428761v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:59,756] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:59,760] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:59,760] [INFO] Target genome list was writen to GCF_014287615.1_ASM1428761v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:59,765] [INFO] Task started: fastANI
[2024-01-24 13:41:59,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg542389af-036a-4091-9baf-0d73b66c36f6/GCF_014287615.1_ASM1428761v1_genomic.fna.gz --refList GCF_014287615.1_ASM1428761v1_genomic.fna/target_genomes.txt --output GCF_014287615.1_ASM1428761v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:13,182] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:13,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d5f1803-ba20-441a-9458-9e1dc558b956/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:13,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d5f1803-ba20-441a-9458-9e1dc558b956/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:13,203] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:42:13,203] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:42:13,204] [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
Blautia producta	strain=JCM 1471	GCA_010669205.1	33035	33035	suspected-type	True	85.7418	1330	2041	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_014131715.1	33035	33035	suspected-type	True	85.7309	1348	2041	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	85.6966	1328	2041	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	85.6847	1338	2041	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	85.5645	1186	2041	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	85.5378	1334	2041	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	85.494	1213	2041	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	85.4889	1203	2041	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	84.882	1352	2041	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	77.948	155	2041	95	below_threshold
Clostridium porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	77.6958	72	2041	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.5814	132	2041	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:13,206] [INFO] DFAST Taxonomy check result was written to GCF_014287615.1_ASM1428761v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:13,206] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:13,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:13,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d5f1803-ba20-441a-9458-9e1dc558b956/dqc_reference/checkm_data
[2024-01-24 13:42:13,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:13,265] [INFO] Task started: CheckM
[2024-01-24 13:42:13,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287615.1_ASM1428761v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287615.1_ASM1428761v1_genomic.fna/checkm_input GCF_014287615.1_ASM1428761v1_genomic.fna/checkm_result
[2024-01-24 13:43:02,236] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:02,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:02,257] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:02,257] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:02,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287615.1_ASM1428761v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:02,258] [INFO] Task started: Blastn
[2024-01-24 13:43:02,258] [INFO] Running command: blastn -query GCF_014287615.1_ASM1428761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d5f1803-ba20-441a-9458-9e1dc558b956/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287615.1_ASM1428761v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:03,354] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:03,359] [INFO] Selected 10 target genomes.
[2024-01-24 13:43:03,359] [INFO] Target genome list was writen to GCF_014287615.1_ASM1428761v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:03,367] [INFO] Task started: fastANI
[2024-01-24 13:43:03,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg542389af-036a-4091-9baf-0d73b66c36f6/GCF_014287615.1_ASM1428761v1_genomic.fna.gz --refList GCF_014287615.1_ASM1428761v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287615.1_ASM1428761v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:13,004] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:13,019] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:13,019] [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_014287615.1	s__Blautia sp001304935	100.0	2040	2041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.32	98.73	0.92	0.87	9	conclusive
GCF_900461125.1	s__Blautia coccoides	85.5425	1350	2041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.33	97.47	0.84	0.79	11	-
GCF_001689125.2	s__Blautia pseudococcoides	85.4967	1203	2041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.82	99.56	0.97	0.91	7	-
GCA_002270465.1	s__Blautia hominis	85.0584	1260	2041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.84	98.04	0.89	0.81	4	-
GCF_003287895.1	s__Blautia argi	78.7909	252	2041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.70	99.67	0.92	0.84	5	-
GCA_003481745.1	s__Blautia stercoris	78.3546	197	2041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.69	97.83	0.91	0.84	8	-
GCA_019119975.1	s__Blautia merdavium	77.8492	245	2041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000469345.1	s__Eubacterium_I ramulus	77.7007	89	2041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	98.54	98.22	0.85	0.78	13	-
GCA_900765525.1	s__Blautia pullicola	77.5048	200	2041	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.10	98.67	0.84	0.76	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:13,021] [INFO] GTDB search result was written to GCF_014287615.1_ASM1428761v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:13,021] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:13,024] [INFO] DFAST_QC result json was written to GCF_014287615.1_ASM1428761v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:13,025] [INFO] DFAST_QC completed!
[2024-01-24 13:43:13,025] [INFO] Total running time: 0h1m32s