[2024-01-24 12:53:56,782] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:56,786] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:56,786] [INFO] DQC Reference Directory: /var/lib/cwl/stga7d57d0d-9c0c-4267-a6f5-b6a14e13ac7e/dqc_reference
[2024-01-24 12:53:58,160] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,161] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,161] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd02086a-d941-413e-a6ac-f841e1216c98/GCF_004011155.1_ASM401115v1_genomic.fna.gz | prodigal -d GCF_004011155.1_ASM401115v1_genomic.fna/cds.fna -a GCF_004011155.1_ASM401115v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:01,954] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:01,954] [INFO] Task started: HMMsearch
[2024-01-24 12:54:01,954] [INFO] Running command: hmmsearch --tblout GCF_004011155.1_ASM401115v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7d57d0d-9c0c-4267-a6f5-b6a14e13ac7e/dqc_reference/reference_markers.hmm GCF_004011155.1_ASM401115v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:02,240] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:02,241] [INFO] Found 6/6 markers.
[2024-01-24 12:54:02,266] [INFO] Query marker FASTA was written to GCF_004011155.1_ASM401115v1_genomic.fna/markers.fasta
[2024-01-24 12:54:02,266] [INFO] Task started: Blastn
[2024-01-24 12:54:02,266] [INFO] Running command: blastn -query GCF_004011155.1_ASM401115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7d57d0d-9c0c-4267-a6f5-b6a14e13ac7e/dqc_reference/reference_markers.fasta -out GCF_004011155.1_ASM401115v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:02,850] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:02,855] [INFO] Selected 26 target genomes.
[2024-01-24 12:54:02,855] [INFO] Target genome list was writen to GCF_004011155.1_ASM401115v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:02,935] [INFO] Task started: fastANI
[2024-01-24 12:54:02,936] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd02086a-d941-413e-a6ac-f841e1216c98/GCF_004011155.1_ASM401115v1_genomic.fna.gz --refList GCF_004011155.1_ASM401115v1_genomic.fna/target_genomes.txt --output GCF_004011155.1_ASM401115v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:19,459] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:19,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7d57d0d-9c0c-4267-a6f5-b6a14e13ac7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:19,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7d57d0d-9c0c-4267-a6f5-b6a14e13ac7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:19,481] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:19,481] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:19,481] [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
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	100.0	846	846	95	conclusive
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	77.3333	218	846	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	76.7124	209	846	95	below_threshold
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	76.6245	234	846	95	below_threshold
Clostridium liquoris	strain=DSM 100320	GCA_002995785.1	1289519	1289519	type	True	76.5909	153	846	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	76.5081	226	846	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_000175595.1	217159	217159	type	True	76.4558	217	846	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	76.3946	172	846	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	76.3686	177	846	95	below_threshold
Haloimpatiens massiliensis	strain=Mt13	GCA_900184255.1	1658110	1658110	type	True	76.3643	175	846	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	76.3241	175	846	95	below_threshold
Clostridium pasteurianum	strain=ATCC 6013	GCA_001856645.1	1501	1501	type	True	76.2163	183	846	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000330945.1	1501	1501	type	True	76.1955	181	846	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000807255.1	1501	1501	type	True	76.1897	188	846	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	76.1648	202	846	95	below_threshold
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	76.1627	206	846	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	76.1552	204	846	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	76.1189	155	846	95	below_threshold
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	76.0916	133	846	95	below_threshold
Clostridium hydrogenum	strain=CUEA01	GCA_021432385.1	2855764	2855764	type	True	76.0406	177	846	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	76.0331	159	846	95	below_threshold
Clostridium polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	75.9648	135	846	95	below_threshold
Clostridium algidicarnis	strain=DSM 15099	GCA_002934235.1	37659	37659	type	True	75.9213	131	846	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	75.7632	187	846	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	75.734	127	846	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	75.2343	118	846	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:19,484] [INFO] DFAST Taxonomy check result was written to GCF_004011155.1_ASM401115v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:19,484] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:19,484] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:19,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7d57d0d-9c0c-4267-a6f5-b6a14e13ac7e/dqc_reference/checkm_data
[2024-01-24 12:54:19,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:19,515] [INFO] Task started: CheckM
[2024-01-24 12:54:19,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004011155.1_ASM401115v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004011155.1_ASM401115v1_genomic.fna/checkm_input GCF_004011155.1_ASM401115v1_genomic.fna/checkm_result
[2024-01-24 12:54:38,383] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:38,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:38,403] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:38,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:38,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004011155.1_ASM401115v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:38,404] [INFO] Task started: Blastn
[2024-01-24 12:54:38,404] [INFO] Running command: blastn -query GCF_004011155.1_ASM401115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7d57d0d-9c0c-4267-a6f5-b6a14e13ac7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004011155.1_ASM401115v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:39,195] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:39,200] [INFO] Selected 23 target genomes.
[2024-01-24 12:54:39,200] [INFO] Target genome list was writen to GCF_004011155.1_ASM401115v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:39,243] [INFO] Task started: fastANI
[2024-01-24 12:54:39,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd02086a-d941-413e-a6ac-f841e1216c98/GCF_004011155.1_ASM401115v1_genomic.fna.gz --refList GCF_004011155.1_ASM401115v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004011155.1_ASM401115v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:52,516] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:52,531] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:52,532] [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_900167505.1	s__F0540 sp900167505	98.8178	763	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	98.87	98.87	0.90	0.90	2	conclusive
GCF_016765585.1	s__F0540 sp016765585	77.8002	277	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000466585.1	s__F0540 sp000466585	77.7368	249	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002008345.1	s__Clostridium_F tepidum	76.6901	211	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
GCF_000968375.1	s__Clostridium_AM scatologenes	76.6342	233	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	N/A	N/A	N/A	N/A	1	-
GCF_900185645.1	s__Clostridium_AK sp900185645	76.543	154	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	96.24	95.22	0.84	0.82	3	-
GCF_001758365.1	s__Clostridium_C acetireducens	76.521	199	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038625.1	s__Clostridium_AM carboxidivorans	76.4987	227	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.96	1.00	0.99	3	-
GCF_900184255.1	s__Haloimpatiens massiliensis	76.4036	175	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Haloimpatiens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129365.1	s__Clostridium_AH fallax	76.3954	172	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AH	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000014125.1	s__Clostridium_H novyi	76.3159	146	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.92	96.35	0.94	0.92	7	-
GCF_001889325.1	s__Clostridium_F botulinum_A	76.2586	210	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	95.92	95.51	0.89	0.85	52	-
GCF_000807255.1	s__Clostridium_I pasteurianum	76.2091	186	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	99.98	99.90	1.00	0.99	7	-
GCF_002285495.1	s__Clostridium isatidis	76.1031	132	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.19	99.19	0.81	0.81	2	-
GCF_015550425.1	s__Clostridium sp015550425	76.0636	139	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.01	99.01	0.93	0.93	2	-
GCF_002934235.1	s__Clostridium_L algidicarnis	75.9333	130	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	97.66	96.15	0.89	0.86	14	-
GCF_018332455.1	s__Clostridium_AR polyendosporum	75.9255	134	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003606265.1	s__Clostridium septicum	75.855	145	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.65	99.48	0.94	0.92	5	-
GCF_900141845.1	s__Clostridium_AG cavendishii	75.7632	187	846	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AG	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:52,534] [INFO] GTDB search result was written to GCF_004011155.1_ASM401115v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:52,535] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:52,540] [INFO] DFAST_QC result json was written to GCF_004011155.1_ASM401115v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:52,541] [INFO] DFAST_QC completed!
[2024-01-24 12:54:52,541] [INFO] Total running time: 0h0m56s