[2024-01-24 11:06:04,655] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:06:04,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:06:04,657] [INFO] DQC Reference Directory: /var/lib/cwl/stgd262a352-cd2e-4520-be03-d0b8fce941f8/dqc_reference
[2024-01-24 11:06:07,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:06:07,011] [INFO] Task started: Prodigal
[2024-01-24 11:06:07,012] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d55fb59-86e5-45ee-a491-ada12518f33d/GCF_025149285.1_ASM2514928v1_genomic.fna.gz | prodigal -d GCF_025149285.1_ASM2514928v1_genomic.fna/cds.fna -a GCF_025149285.1_ASM2514928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:24,282] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:24,283] [INFO] Task started: HMMsearch
[2024-01-24 11:06:24,283] [INFO] Running command: hmmsearch --tblout GCF_025149285.1_ASM2514928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd262a352-cd2e-4520-be03-d0b8fce941f8/dqc_reference/reference_markers.hmm GCF_025149285.1_ASM2514928v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:24,622] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:24,623] [INFO] Found 6/6 markers.
[2024-01-24 11:06:24,676] [INFO] Query marker FASTA was written to GCF_025149285.1_ASM2514928v1_genomic.fna/markers.fasta
[2024-01-24 11:06:24,677] [INFO] Task started: Blastn
[2024-01-24 11:06:24,677] [INFO] Running command: blastn -query GCF_025149285.1_ASM2514928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd262a352-cd2e-4520-be03-d0b8fce941f8/dqc_reference/reference_markers.fasta -out GCF_025149285.1_ASM2514928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:25,344] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:25,347] [INFO] Selected 16 target genomes.
[2024-01-24 11:06:25,347] [INFO] Target genome list was writen to GCF_025149285.1_ASM2514928v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:25,353] [INFO] Task started: fastANI
[2024-01-24 11:06:25,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d55fb59-86e5-45ee-a491-ada12518f33d/GCF_025149285.1_ASM2514928v1_genomic.fna.gz --refList GCF_025149285.1_ASM2514928v1_genomic.fna/target_genomes.txt --output GCF_025149285.1_ASM2514928v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:40,259] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:40,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd262a352-cd2e-4520-be03-d0b8fce941f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:40,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd262a352-cd2e-4520-be03-d0b8fce941f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:40,276] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:06:40,276] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:40,276] [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
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	100.0	2309	2310	95	conclusive
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	99.533	1977	2310	95	conclusive
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	87.1686	1493	2310	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	82.8951	158	2310	95	below_threshold
Coprococcus catus	strain=ATCC 27761	GCA_025289135.1	116085	116085	suspected-type	True	81.8033	72	2310	95	below_threshold
Anaerostipes caccae	strain=DSM 14662	GCA_025146005.1	105841	105841	type	True	79.3785	69	2310	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	78.8155	56	2310	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	78.698	230	2310	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	78.6597	293	2310	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	78.5569	295	2310	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	78.3956	213	2310	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	78.3653	113	2310	95	below_threshold
Lachnoclostridium pacaense	strain=Marseille-P3100	GCA_900566185.1	1917870	1917870	type	True	78.0974	87	2310	95	below_threshold
Lacrimispora algidixylanolytica	strain=SPL73	GCA_003609635.1	94868	94868	type	True	78.0471	183	2310	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:40,277] [INFO] DFAST Taxonomy check result was written to GCF_025149285.1_ASM2514928v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:40,278] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:40,278] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:40,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd262a352-cd2e-4520-be03-d0b8fce941f8/dqc_reference/checkm_data
[2024-01-24 11:06:40,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:40,342] [INFO] Task started: CheckM
[2024-01-24 11:06:40,343] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025149285.1_ASM2514928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025149285.1_ASM2514928v1_genomic.fna/checkm_input GCF_025149285.1_ASM2514928v1_genomic.fna/checkm_result
[2024-01-24 11:07:33,258] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:33,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:33,279] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:33,279] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:33,279] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025149285.1_ASM2514928v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:33,279] [INFO] Task started: Blastn
[2024-01-24 11:07:33,280] [INFO] Running command: blastn -query GCF_025149285.1_ASM2514928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd262a352-cd2e-4520-be03-d0b8fce941f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_025149285.1_ASM2514928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:34,366] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:34,369] [INFO] Selected 19 target genomes.
[2024-01-24 11:07:34,370] [INFO] Target genome list was writen to GCF_025149285.1_ASM2514928v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:34,398] [INFO] Task started: fastANI
[2024-01-24 11:07:34,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d55fb59-86e5-45ee-a491-ada12518f33d/GCF_025149285.1_ASM2514928v1_genomic.fna.gz --refList GCF_025149285.1_ASM2514928v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025149285.1_ASM2514928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:51,110] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:51,132] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:51,132] [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_005845265.1	s__Hungatella sp005845265	98.768	1759	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella	95.0	98.89	98.68	0.87	0.80	12	conclusive
GCF_003201875.1	s__Hungatella effluvii	87.1704	1492	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella	95.0	95.81	95.49	0.78	0.75	20	-
GCF_000235505.1	s__Hungatella_A hathewayi_A	80.0235	334	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella_A	95.0	99.27	96.59	0.97	0.86	6	-
GCA_000155435.1	s__Enterocloster sp000155435	79.2821	248	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.08	98.70	0.90	0.83	5	-
GCF_003480435.1	s__Copromonas sp900066055	79.0391	132	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.09	96.90	0.88	0.80	7	-
GCF_900155545.1	s__Lacrimispora sp900155545	78.7819	352	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002899675.1	s__CHH4-2 sp002899675	78.5656	267	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CHH4-2	95.0	100.00	100.00	0.98	0.98	2	-
GCA_017084465.1	s__Lacrimispora xylanolytica_B	78.4283	267	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.07	99.07	0.96	0.96	2	-
GCF_013036995.1	s__Lacrimispora xylanolytica_A	78.1917	255	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057705.1	s__Lacrimispora sp015057705	78.0919	246	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363835.1	s__Lacrimispora sp902363835	78.0839	326	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003434055.1	s__Enterocloster aldenensis	78.0298	196	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.16	97.51	0.89	0.78	13	-
GCA_905215155.1	s__Lacrimispora sp905215155	78.0175	262	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057715.1	s__Lacrimispora sp015057715	77.9809	240	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363735.1	s__Lacrimispora sp902363735	77.9219	224	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057775.1	s__Lacrimispora sp015057775	77.8421	223	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002389905.1	s__Lacrimispora sp002389905	77.8127	274	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114305.1	s__Hungatella pullicola	77.462	198	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella	95.0	99.96	99.96	0.96	0.96	2	-
GCA_017556515.1	s__Copromonas sp017556515	76.8309	51	2310	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:51,134] [INFO] GTDB search result was written to GCF_025149285.1_ASM2514928v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:51,134] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:51,139] [INFO] DFAST_QC result json was written to GCF_025149285.1_ASM2514928v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:51,139] [INFO] DFAST_QC completed!
[2024-01-24 11:07:51,139] [INFO] Total running time: 0h1m46s