[2024-01-24 11:21:07,406] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg492320ca-d7d1-439f-813b-504345f3d5c0/dqc_reference
[2024-01-24 11:21:11,960] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,961] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,962] [INFO] Running command: gunzip -c /var/lib/cwl/stg796c0258-9d08-48c4-863e-034e56b846e3/GCF_014385265.1_ASM1438526v1_genomic.fna.gz | prodigal -d GCF_014385265.1_ASM1438526v1_genomic.fna/cds.fna -a GCF_014385265.1_ASM1438526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:19,227] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:19,228] [INFO] Task started: HMMsearch
[2024-01-24 11:21:19,228] [INFO] Running command: hmmsearch --tblout GCF_014385265.1_ASM1438526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg492320ca-d7d1-439f-813b-504345f3d5c0/dqc_reference/reference_markers.hmm GCF_014385265.1_ASM1438526v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:19,462] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:19,464] [INFO] Found 6/6 markers.
[2024-01-24 11:21:19,492] [INFO] Query marker FASTA was written to GCF_014385265.1_ASM1438526v1_genomic.fna/markers.fasta
[2024-01-24 11:21:19,492] [INFO] Task started: Blastn
[2024-01-24 11:21:19,492] [INFO] Running command: blastn -query GCF_014385265.1_ASM1438526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg492320ca-d7d1-439f-813b-504345f3d5c0/dqc_reference/reference_markers.fasta -out GCF_014385265.1_ASM1438526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:20,083] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:20,087] [INFO] Selected 23 target genomes.
[2024-01-24 11:21:20,088] [INFO] Target genome list was writen to GCF_014385265.1_ASM1438526v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:20,213] [INFO] Task started: fastANI
[2024-01-24 11:21:20,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg796c0258-9d08-48c4-863e-034e56b846e3/GCF_014385265.1_ASM1438526v1_genomic.fna.gz --refList GCF_014385265.1_ASM1438526v1_genomic.fna/target_genomes.txt --output GCF_014385265.1_ASM1438526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:35,636] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:35,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg492320ca-d7d1-439f-813b-504345f3d5c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:35,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg492320ca-d7d1-439f-813b-504345f3d5c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:35,651] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:21:35,651] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:21:35,651] [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	78.1118	106	914	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_900129135.1	341220	341220	suspected-type	True	77.9062	54	914	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	77.8673	95	914	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	77.3221	78	914	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	77.3015	170	914	95	below_threshold
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	77.2841	61	914	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	77.2266	168	914	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.1933	78	914	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	77.1518	98	914	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	76.9587	77	914	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.842	120	914	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.8021	69	914	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.7957	119	914	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	76.7739	72	914	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	76.7587	50	914	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.6494	123	914	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.6292	66	914	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:35,653] [INFO] DFAST Taxonomy check result was written to GCF_014385265.1_ASM1438526v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:35,653] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:35,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:35,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg492320ca-d7d1-439f-813b-504345f3d5c0/dqc_reference/checkm_data
[2024-01-24 11:21:35,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:35,683] [INFO] Task started: CheckM
[2024-01-24 11:21:35,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014385265.1_ASM1438526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014385265.1_ASM1438526v1_genomic.fna/checkm_input GCF_014385265.1_ASM1438526v1_genomic.fna/checkm_result
[2024-01-24 11:22:02,080] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:02,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:02,102] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:02,103] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:02,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014385265.1_ASM1438526v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:02,104] [INFO] Task started: Blastn
[2024-01-24 11:22:02,104] [INFO] Running command: blastn -query GCF_014385265.1_ASM1438526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg492320ca-d7d1-439f-813b-504345f3d5c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014385265.1_ASM1438526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:03,005] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:03,009] [INFO] Selected 14 target genomes.
[2024-01-24 11:22:03,010] [INFO] Target genome list was writen to GCF_014385265.1_ASM1438526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:03,025] [INFO] Task started: fastANI
[2024-01-24 11:22:03,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg796c0258-9d08-48c4-863e-034e56b846e3/GCF_014385265.1_ASM1438526v1_genomic.fna.gz --refList GCF_014385265.1_ASM1438526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014385265.1_ASM1438526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:11,240] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:11,253] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:11,253] [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_014385265.1	s__Copromonas sp000435795	100.0	913	914	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.24	96.73	0.89	0.84	6	conclusive
GCA_905215775.1	s__Copromonas sp905215775	91.1259	690	914	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003478035.1	s__Copromonas sp900066785	78.9599	230	914	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	97.14	96.17	0.83	0.76	16	-
GCF_003435375.1	s__Copromonas sp900066535	78.7769	240	914	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	97.23	95.52	0.82	0.74	22	-
GCA_018223415.1	s__Copromonas sp900541255	78.7529	318	914	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	99.81	99.68	0.96	0.93	4	-
GCF_003480435.1	s__Copromonas sp900066055	78.5915	233	914	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.09	96.90	0.88	0.80	7	-
GCA_910586315.1	s__Copromonas sp910586315	78.5325	272	914	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585355.1	s__Copromonas sp910585355	78.3769	275	914	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556965.1	s__Copromonas sp900556965	77.8746	126	914	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715565.1	s__Ventrimonas merdavium	77.3907	178	914	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_019114845.1	s__Lachnoclostridium_A stercoripullorum	77.0946	165	914	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.44	98.44	0.80	0.80	2	-
GCA_910585635.1	s__Caccovicinus sp910585635	76.8646	141	914	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002899675.1	s__CHH4-2 sp002899675	76.6956	93	914	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	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:11,255] [INFO] GTDB search result was written to GCF_014385265.1_ASM1438526v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:11,255] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:11,258] [INFO] DFAST_QC result json was written to GCF_014385265.1_ASM1438526v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:11,259] [INFO] DFAST_QC completed!
[2024-01-24 11:22:11,259] [INFO] Total running time: 0h1m4s