[2024-01-24 12:40:04,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:04,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:04,075] [INFO] DQC Reference Directory: /var/lib/cwl/stgf321b763-566d-431b-a2b4-aa5dca05a04e/dqc_reference
[2024-01-24 12:40:05,266] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:05,266] [INFO] Task started: Prodigal
[2024-01-24 12:40:05,267] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bfcb212-7ce3-492a-8407-74fdeb256d77/GCF_019042245.1_ASM1904224v1_genomic.fna.gz | prodigal -d GCF_019042245.1_ASM1904224v1_genomic.fna/cds.fna -a GCF_019042245.1_ASM1904224v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:18,900] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:18,901] [INFO] Task started: HMMsearch
[2024-01-24 12:40:18,901] [INFO] Running command: hmmsearch --tblout GCF_019042245.1_ASM1904224v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf321b763-566d-431b-a2b4-aa5dca05a04e/dqc_reference/reference_markers.hmm GCF_019042245.1_ASM1904224v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:19,232] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:19,233] [INFO] Found 6/6 markers.
[2024-01-24 12:40:19,282] [INFO] Query marker FASTA was written to GCF_019042245.1_ASM1904224v1_genomic.fna/markers.fasta
[2024-01-24 12:40:19,283] [INFO] Task started: Blastn
[2024-01-24 12:40:19,283] [INFO] Running command: blastn -query GCF_019042245.1_ASM1904224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf321b763-566d-431b-a2b4-aa5dca05a04e/dqc_reference/reference_markers.fasta -out GCF_019042245.1_ASM1904224v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:19,933] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:19,937] [INFO] Selected 20 target genomes.
[2024-01-24 12:40:19,937] [INFO] Target genome list was writen to GCF_019042245.1_ASM1904224v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:19,948] [INFO] Task started: fastANI
[2024-01-24 12:40:19,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bfcb212-7ce3-492a-8407-74fdeb256d77/GCF_019042245.1_ASM1904224v1_genomic.fna.gz --refList GCF_019042245.1_ASM1904224v1_genomic.fna/target_genomes.txt --output GCF_019042245.1_ASM1904224v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:35,001] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:35,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf321b763-566d-431b-a2b4-aa5dca05a04e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:35,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf321b763-566d-431b-a2b4-aa5dca05a04e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:35,018] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:35,018] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:35,019] [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
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	100.0	1834	1837	95	conclusive
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	88.3897	1295	1837	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	77.9177	76	1837	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	76.5949	52	1837	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	76.4978	76	1837	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	76.4676	81	1837	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	76.4676	81	1837	95	below_threshold
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	76.3171	87	1837	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	76.2449	70	1837	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	76.2318	86	1837	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.1947	72	1837	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.1792	73	1837	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.1169	94	1837	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	76.1051	83	1837	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:35,020] [INFO] DFAST Taxonomy check result was written to GCF_019042245.1_ASM1904224v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:35,020] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:35,021] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:35,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf321b763-566d-431b-a2b4-aa5dca05a04e/dqc_reference/checkm_data
[2024-01-24 12:40:35,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:35,084] [INFO] Task started: CheckM
[2024-01-24 12:40:35,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019042245.1_ASM1904224v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019042245.1_ASM1904224v1_genomic.fna/checkm_input GCF_019042245.1_ASM1904224v1_genomic.fna/checkm_result
[2024-01-24 12:41:18,532] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:18,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:18,559] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:18,559] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:18,560] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019042245.1_ASM1904224v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:18,560] [INFO] Task started: Blastn
[2024-01-24 12:41:18,561] [INFO] Running command: blastn -query GCF_019042245.1_ASM1904224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf321b763-566d-431b-a2b4-aa5dca05a04e/dqc_reference/reference_markers_gtdb.fasta -out GCF_019042245.1_ASM1904224v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:19,652] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:19,656] [INFO] Selected 22 target genomes.
[2024-01-24 12:41:19,656] [INFO] Target genome list was writen to GCF_019042245.1_ASM1904224v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:19,683] [INFO] Task started: fastANI
[2024-01-24 12:41:19,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bfcb212-7ce3-492a-8407-74fdeb256d77/GCF_019042245.1_ASM1904224v1_genomic.fna.gz --refList GCF_019042245.1_ASM1904224v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019042245.1_ASM1904224v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:34,080] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:34,105] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:34,105] [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_902363085.1	s__GCA-900066755 sp902363085	99.708	1697	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__GCA-900066755	95.0	99.73	99.73	0.92	0.92	2	conclusive
GCA_902362855.1	s__GCA-900066755 sp900066755	88.311	1315	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__GCA-900066755	95.0	99.21	98.73	0.90	0.82	4	-
GCF_014290175.1	s__Merdisoma sp014290175	78.1951	83	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.98	99.96	0.81	0.62	3	-
GCA_018223385.1	s__JAGTTR01 sp018223385	76.6903	91	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAGTTR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001689125.2	s__Blautia pseudococcoides	76.4725	83	1837	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_000403295.2	s__Schaedlerella sp000403295	76.3594	69	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.10	98.10	0.85	0.85	2	-
GCA_910574835.1	s__Merdisoma sp910574835	76.3396	81	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542045.1	s__Blautia_A gallistercoris	76.3248	73	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.42	98.42	0.88	0.88	2	-
GCA_004793545.1	s__14-2 sp004793545	76.1508	64	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161285.1	s__Blautia ornithocaccae	76.1354	64	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.34	98.05	0.87	0.83	4	-
GCF_000403455.2	s__Sporofaciens sp000403455	76.1007	63	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.91	98.91	0.91	0.91	2	-
GCA_019118525.1	s__Bariatricus faecipullorum	76.0314	62	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016297895.1	s__Marvinbryantia sp016297895	76.0135	56	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214955.1	s__Limivivens sp905214955	75.9277	57	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715565.1	s__Ventrimonas merdavium	75.8752	64	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.46	99.46	0.97	0.97	2	-
GCA_900543715.1	s__Blautia merdigallinarum	75.7964	50	1837	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.67	98.67	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:34,108] [INFO] GTDB search result was written to GCF_019042245.1_ASM1904224v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:34,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:34,111] [INFO] DFAST_QC result json was written to GCF_019042245.1_ASM1904224v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:34,111] [INFO] DFAST_QC completed!
[2024-01-24 12:41:34,112] [INFO] Total running time: 0h1m30s