[2024-01-24 14:55:18,642] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:18,643] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:18,643] [INFO] DQC Reference Directory: /var/lib/cwl/stg3af1bf40-5246-4b8a-993a-cf79b63afe7a/dqc_reference
[2024-01-24 14:55:19,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:19,955] [INFO] Task started: Prodigal
[2024-01-24 14:55:19,955] [INFO] Running command: gunzip -c /var/lib/cwl/stg16f7b06a-81d3-4fb0-8302-1f9fd5721e0e/GCF_003600355.1_ASM360035v1_genomic.fna.gz | prodigal -d GCF_003600355.1_ASM360035v1_genomic.fna/cds.fna -a GCF_003600355.1_ASM360035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:25,099] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:25,099] [INFO] Task started: HMMsearch
[2024-01-24 14:55:25,099] [INFO] Running command: hmmsearch --tblout GCF_003600355.1_ASM360035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3af1bf40-5246-4b8a-993a-cf79b63afe7a/dqc_reference/reference_markers.hmm GCF_003600355.1_ASM360035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:25,394] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:25,395] [INFO] Found 6/6 markers.
[2024-01-24 14:55:25,420] [INFO] Query marker FASTA was written to GCF_003600355.1_ASM360035v1_genomic.fna/markers.fasta
[2024-01-24 14:55:25,421] [INFO] Task started: Blastn
[2024-01-24 14:55:25,421] [INFO] Running command: blastn -query GCF_003600355.1_ASM360035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3af1bf40-5246-4b8a-993a-cf79b63afe7a/dqc_reference/reference_markers.fasta -out GCF_003600355.1_ASM360035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:26,045] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:26,049] [INFO] Selected 24 target genomes.
[2024-01-24 14:55:26,049] [INFO] Target genome list was writen to GCF_003600355.1_ASM360035v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:26,063] [INFO] Task started: fastANI
[2024-01-24 14:55:26,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg16f7b06a-81d3-4fb0-8302-1f9fd5721e0e/GCF_003600355.1_ASM360035v1_genomic.fna.gz --refList GCF_003600355.1_ASM360035v1_genomic.fna/target_genomes.txt --output GCF_003600355.1_ASM360035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:45,074] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:45,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3af1bf40-5246-4b8a-993a-cf79b63afe7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:45,075] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3af1bf40-5246-4b8a-993a-cf79b63afe7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:45,096] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:45,097] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:45,097] [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 fermenticellae	strain=JN500901	GCA_003600355.1	2068654	2068654	type	True	100.0	939	939	95	conclusive
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	78.7986	316	939	95	below_threshold
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	78.6906	327	939	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	78.4765	322	939	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	78.2502	281	939	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_000175595.1	217159	217159	type	True	78.1096	291	939	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	78.0507	77	939	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	78.0285	242	939	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	77.7008	172	939	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	77.6458	172	939	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	77.4863	258	939	95	below_threshold
Clostridium aciditolerans	strain=DSM 17425	GCA_016316925.1	339861	339861	type	True	77.4678	200	939	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	77.459	123	939	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	77.3516	122	939	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	77.3321	127	939	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	77.2599	121	939	95	below_threshold
Clostridium tyrobutyricum	strain=ATCC 25755	GCA_000359585.1	1519	1519	type	True	76.9338	152	939	95	below_threshold
Clostridium tyrobutyricum	strain=DSM 2637	GCA_000429805.1	1519	1519	type	True	76.9311	157	939	95	below_threshold
Clostridium tyrobutyricum	strain=DSM 2637	GCA_000392375.2	1519	1519	type	True	76.8794	150	939	95	below_threshold
Clostridium liquoris	strain=DSM 100320	GCA_002995785.1	1289519	1289519	type	True	76.8653	119	939	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	75.5066	87	939	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:45,099] [INFO] DFAST Taxonomy check result was written to GCF_003600355.1_ASM360035v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:45,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:45,104] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:45,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3af1bf40-5246-4b8a-993a-cf79b63afe7a/dqc_reference/checkm_data
[2024-01-24 14:55:45,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:45,148] [INFO] Task started: CheckM
[2024-01-24 14:55:45,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003600355.1_ASM360035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003600355.1_ASM360035v1_genomic.fna/checkm_input GCF_003600355.1_ASM360035v1_genomic.fna/checkm_result
[2024-01-24 14:56:06,974] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:06,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:06,994] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:06,995] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:06,995] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003600355.1_ASM360035v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:06,996] [INFO] Task started: Blastn
[2024-01-24 14:56:06,996] [INFO] Running command: blastn -query GCF_003600355.1_ASM360035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3af1bf40-5246-4b8a-993a-cf79b63afe7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003600355.1_ASM360035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:07,779] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:07,782] [INFO] Selected 18 target genomes.
[2024-01-24 14:56:07,782] [INFO] Target genome list was writen to GCF_003600355.1_ASM360035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:07,812] [INFO] Task started: fastANI
[2024-01-24 14:56:07,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg16f7b06a-81d3-4fb0-8302-1f9fd5721e0e/GCF_003600355.1_ASM360035v1_genomic.fna.gz --refList GCF_003600355.1_ASM360035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003600355.1_ASM360035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:22,087] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:22,105] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:22,106] [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_003600355.1	s__JN-1 sp003600355	100.0	939	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__JN-1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003718715.1	s__JN-1 sp003718715	81.505	534	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__JN-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000968375.1	s__Clostridium_AM scatologenes	78.6345	323	939	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_001038625.1	s__Clostridium_AM carboxidivorans	78.5282	319	939	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_000633595.2	s__Clostridium_AM drakei	78.3339	300	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	100.00	100.00	1.00	1.00	2	-
GCF_012926525.1	s__Clostridium_AM sp012926525	78.27	280	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143685.1	s__Clostridium_B ljungdahlii	78.0327	254	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	98.76	97.79	0.92	0.88	9	-
GCF_004006395.2	s__Clostridium_B sp004006395	77.9592	235	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016505.1	s__Clostridium_B kluyveri	77.6967	173	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	97.52	95.05	0.91	0.81	3	-
GCF_019207025.1	s__Clostridium_AM sp019207025	77.493	258	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016316925.1	s__Clostridium_AM aciditolerans	77.4678	200	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	95.27	95.27	0.80	0.80	2	-
GCF_014050525.1	s__Clostridium_B sp014050525	76.9455	170	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000359585.1	s__Clostridium_B tyrobutyricum	76.9338	152	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	99.17	95.02	0.91	0.82	32	-
GCF_002995785.1	s__Clostridium_AO liquoris	76.8653	119	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758365.1	s__Clostridium_C acetireducens	76.7497	140	939	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_900095445.1	s__UBA3947 sp900095445	76.2449	62	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__UBA3947	95.0	99.63	99.63	0.84	0.84	2	-
GCA_902785295.1	s__Clostridium sp902785295	75.9768	69	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:22,107] [INFO] GTDB search result was written to GCF_003600355.1_ASM360035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:22,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:22,111] [INFO] DFAST_QC result json was written to GCF_003600355.1_ASM360035v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:22,112] [INFO] DFAST_QC completed!
[2024-01-24 14:56:22,112] [INFO] Total running time: 0h1m3s