[2024-01-24 14:05:31,894] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:31,895] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:31,896] [INFO] DQC Reference Directory: /var/lib/cwl/stg043fd263-f7ad-4d4f-9b45-484e17cc3c70/dqc_reference
[2024-01-24 14:05:33,049] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:33,050] [INFO] Task started: Prodigal
[2024-01-24 14:05:33,050] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f86c429-a502-4ba0-90f6-87cd683a4773/GCF_003201875.1_ASM320187v1_genomic.fna.gz | prodigal -d GCF_003201875.1_ASM320187v1_genomic.fna/cds.fna -a GCF_003201875.1_ASM320187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:49,830] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:49,831] [INFO] Task started: HMMsearch
[2024-01-24 14:05:49,831] [INFO] Running command: hmmsearch --tblout GCF_003201875.1_ASM320187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg043fd263-f7ad-4d4f-9b45-484e17cc3c70/dqc_reference/reference_markers.hmm GCF_003201875.1_ASM320187v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:50,230] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:50,231] [INFO] Found 6/6 markers.
[2024-01-24 14:05:50,293] [INFO] Query marker FASTA was written to GCF_003201875.1_ASM320187v1_genomic.fna/markers.fasta
[2024-01-24 14:05:50,293] [INFO] Task started: Blastn
[2024-01-24 14:05:50,293] [INFO] Running command: blastn -query GCF_003201875.1_ASM320187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg043fd263-f7ad-4d4f-9b45-484e17cc3c70/dqc_reference/reference_markers.fasta -out GCF_003201875.1_ASM320187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:51,033] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:51,036] [INFO] Selected 16 target genomes.
[2024-01-24 14:05:51,037] [INFO] Target genome list was writen to GCF_003201875.1_ASM320187v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:51,043] [INFO] Task started: fastANI
[2024-01-24 14:05:51,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f86c429-a502-4ba0-90f6-87cd683a4773/GCF_003201875.1_ASM320187v1_genomic.fna.gz --refList GCF_003201875.1_ASM320187v1_genomic.fna/target_genomes.txt --output GCF_003201875.1_ASM320187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:07,394] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:07,395] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg043fd263-f7ad-4d4f-9b45-484e17cc3c70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:07,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg043fd263-f7ad-4d4f-9b45-484e17cc3c70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:07,410] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:07,410] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:07,411] [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 effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	100.0	2262	2265	95	conclusive
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	87.1145	1492	2265	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	86.925	1331	2265	95	below_threshold
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	78.4966	228	2265	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	78.2669	293	2265	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	78.2198	294	2265	95	below_threshold
Lacrimispora algidixylanolytica	strain=SPL73	GCA_003609635.1	94868	94868	type	True	77.9726	178	2265	95	below_threshold
Lachnoclostridium pacaense	strain=Marseille-P3100	GCA_900566185.1	1917870	1917870	type	True	77.3086	81	2265	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	77.3069	176	2265	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	77.0909	103	2265	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.9474	89	2265	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.862	227	2265	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.7977	233	2265	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	76.7812	88	2265	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.4704	93	2265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:07,412] [INFO] DFAST Taxonomy check result was written to GCF_003201875.1_ASM320187v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:07,413] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:07,413] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:07,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg043fd263-f7ad-4d4f-9b45-484e17cc3c70/dqc_reference/checkm_data
[2024-01-24 14:06:07,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:07,478] [INFO] Task started: CheckM
[2024-01-24 14:06:07,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003201875.1_ASM320187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003201875.1_ASM320187v1_genomic.fna/checkm_input GCF_003201875.1_ASM320187v1_genomic.fna/checkm_result
[2024-01-24 14:07:01,132] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:01,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:01,155] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:01,155] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:01,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003201875.1_ASM320187v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:01,156] [INFO] Task started: Blastn
[2024-01-24 14:07:01,156] [INFO] Running command: blastn -query GCF_003201875.1_ASM320187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg043fd263-f7ad-4d4f-9b45-484e17cc3c70/dqc_reference/reference_markers_gtdb.fasta -out GCF_003201875.1_ASM320187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:02,221] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:02,225] [INFO] Selected 19 target genomes.
[2024-01-24 14:07:02,226] [INFO] Target genome list was writen to GCF_003201875.1_ASM320187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:02,241] [INFO] Task started: fastANI
[2024-01-24 14:07:02,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f86c429-a502-4ba0-90f6-87cd683a4773/GCF_003201875.1_ASM320187v1_genomic.fna.gz --refList GCF_003201875.1_ASM320187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003201875.1_ASM320187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:19,684] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:19,703] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:19,704] [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_003201875.1	s__Hungatella effluvii	100.0	2262	2265	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella	95.0	95.81	95.49	0.78	0.75	20	conclusive
GCF_005845265.1	s__Hungatella sp005845265	87.1833	1482	2265	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella	95.0	98.89	98.68	0.87	0.80	12	-
GCF_900155545.1	s__Lacrimispora sp900155545	78.6808	343	2265	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_013036995.1	s__Lacrimispora xylanolytica_A	78.3509	230	2265	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_900105215.1	s__Lacrimispora sphenoides_A	78.2908	289	2265	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	96.8556	97.72	97.62	0.92	0.89	4	-
GCA_009712635.1	s__Lacrimispora sp009712635	78.2899	236	2265	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	78.0746	314	2265	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_000526995.1	s__Lacrimispora indolis	78.0595	336	2265	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.32	99.25	0.95	0.92	3	-
GCA_902363735.1	s__Lacrimispora sp902363735	78.0056	218	2265	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	78.0046	260	2265	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_002367105.1	s__Lacrimispora sp002367105	77.9675	284	2265	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_003609635.1	s__Lacrimispora algidixylanolytica	77.9481	180	2265	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_003480435.1	s__Copromonas sp900066055	77.5535	102	2265	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_000155435.1	s__Enterocloster sp000155435	77.5091	213	2265	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_000424325.1	s__Enterocloster clostridioformis_A	77.3722	167	2265	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.02	99.02	0.92	0.92	2	-
GCA_900547735.1	s__Clostridium_Q sp900547735	77.0004	157	2265	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003435375.1	s__Copromonas sp900066535	76.9975	106	2265	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	97.23	95.52	0.82	0.74	22	-
GCF_000158075.1	s__Enterocloster asparagiformis	76.7767	234	2265	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.72	98.33	0.90	0.88	5	-
GCA_017556515.1	s__Copromonas sp017556515	76.3955	59	2265	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 14:07:19,705] [INFO] GTDB search result was written to GCF_003201875.1_ASM320187v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:19,706] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:19,710] [INFO] DFAST_QC result json was written to GCF_003201875.1_ASM320187v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:19,710] [INFO] DFAST_QC completed!
[2024-01-24 14:07:19,710] [INFO] Total running time: 0h1m48s