[2024-01-24 13:57:16,210] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:16,212] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:16,213] [INFO] DQC Reference Directory: /var/lib/cwl/stg67c86689-df67-4124-bc6b-15cdd8a0e13c/dqc_reference
[2024-01-24 13:57:17,616] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:17,622] [INFO] Task started: Prodigal
[2024-01-24 13:57:17,623] [INFO] Running command: gunzip -c /var/lib/cwl/stgeabca44a-0526-427e-b02f-fb16a45588ed/GCF_002050515.1_ASM205051v1_genomic.fna.gz | prodigal -d GCF_002050515.1_ASM205051v1_genomic.fna/cds.fna -a GCF_002050515.1_ASM205051v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:22,511] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:22,511] [INFO] Task started: HMMsearch
[2024-01-24 13:57:22,511] [INFO] Running command: hmmsearch --tblout GCF_002050515.1_ASM205051v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67c86689-df67-4124-bc6b-15cdd8a0e13c/dqc_reference/reference_markers.hmm GCF_002050515.1_ASM205051v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:22,836] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:22,837] [INFO] Found 6/6 markers.
[2024-01-24 13:57:22,873] [INFO] Query marker FASTA was written to GCF_002050515.1_ASM205051v1_genomic.fna/markers.fasta
[2024-01-24 13:57:22,874] [INFO] Task started: Blastn
[2024-01-24 13:57:22,874] [INFO] Running command: blastn -query GCF_002050515.1_ASM205051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67c86689-df67-4124-bc6b-15cdd8a0e13c/dqc_reference/reference_markers.fasta -out GCF_002050515.1_ASM205051v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:23,475] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:23,479] [INFO] Selected 26 target genomes.
[2024-01-24 13:57:23,480] [INFO] Target genome list was writen to GCF_002050515.1_ASM205051v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:23,486] [INFO] Task started: fastANI
[2024-01-24 13:57:23,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgeabca44a-0526-427e-b02f-fb16a45588ed/GCF_002050515.1_ASM205051v1_genomic.fna.gz --refList GCF_002050515.1_ASM205051v1_genomic.fna/target_genomes.txt --output GCF_002050515.1_ASM205051v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:41,537] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:41,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67c86689-df67-4124-bc6b-15cdd8a0e13c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:41,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67c86689-df67-4124-bc6b-15cdd8a0e13c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:41,557] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:41,558] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:41,558] [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 thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	100.0	1065	1081	95	conclusive
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	78.9277	395	1081	95	below_threshold
Clostridium sardiniense	strain=DSM 2632	GCA_016907995.1	29369	29369	type	True	78.8612	422	1081	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	78.398	358	1081	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	77.9607	299	1081	95	below_threshold
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	77.9118	259	1081	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	77.8167	287	1081	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	77.5864	258	1081	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.5637	295	1081	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	77.5303	332	1081	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	77.2786	277	1081	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	77.2016	271	1081	95	below_threshold
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	77.1718	293	1081	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	77.1675	260	1081	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008705175.1	223919	223919	suspected-type	True	77.0747	253	1081	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	76.9389	281	1081	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008580445.1	223919	223919	suspected-type	True	76.9017	248	1081	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	76.8918	251	1081	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	76.8858	246	1081	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	76.01	158	1081	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	76.0087	150	1081	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	75.9884	158	1081	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	75.8029	194	1081	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	74.6894	73	1081	95	below_threshold
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	74.6827	75	1081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:41,567] [INFO] DFAST Taxonomy check result was written to GCF_002050515.1_ASM205051v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:41,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:41,569] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:41,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67c86689-df67-4124-bc6b-15cdd8a0e13c/dqc_reference/checkm_data
[2024-01-24 13:57:41,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:41,613] [INFO] Task started: CheckM
[2024-01-24 13:57:41,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002050515.1_ASM205051v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002050515.1_ASM205051v1_genomic.fna/checkm_input GCF_002050515.1_ASM205051v1_genomic.fna/checkm_result
[2024-01-24 13:58:04,141] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:04,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:04,189] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:04,190] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:04,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002050515.1_ASM205051v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:04,191] [INFO] Task started: Blastn
[2024-01-24 13:58:04,191] [INFO] Running command: blastn -query GCF_002050515.1_ASM205051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67c86689-df67-4124-bc6b-15cdd8a0e13c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002050515.1_ASM205051v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:05,097] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:05,102] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:05,102] [INFO] Target genome list was writen to GCF_002050515.1_ASM205051v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:05,116] [INFO] Task started: fastANI
[2024-01-24 13:58:05,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgeabca44a-0526-427e-b02f-fb16a45588ed/GCF_002050515.1_ASM205051v1_genomic.fna.gz --refList GCF_002050515.1_ASM205051v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002050515.1_ASM205051v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:21,853] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:21,869] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:21,869] [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_002050515.1	s__Clostridium thermobutyricum	100.0	1064	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.10	97.10	0.91	0.89	3	conclusive
GCF_000498355.1	s__Clostridium sp000498355	79.1104	436	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789395.1	s__Clostridium baratii	79.0318	437	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.53	95.37	0.92	0.89	15	-
GCF_017873235.1	s__Clostridium moniliforme	78.8996	399	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907995.1	s__Clostridium sardiniense	78.8479	423	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015234215.1	s__Clostridium sp015234215	78.4424	354	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002327185.1	s__Clostridium chauvoei	77.9827	299	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCF_900290265.1	s__Clostridium cagae	77.8164	287	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.09	97.56	0.90	0.85	15	-
GCF_015555905.1	s__Clostridium sp015555905	77.7305	277	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.95	98.95	0.73	0.73	2	-
GCF_900116755.1	s__Clostridium sp900116755	77.6773	252	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015667795.1	s__Clostridium sp015667795	77.568	318	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015058375.1	s__Clostridium sp015058375	77.5426	199	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588715.1	s__Clostridium sp910588715	77.4384	286	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827935.1	s__Clostridium botulinum_A	77.4243	319	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.05	97.92	0.91	0.85	31	-
GCA_900540255.1	s__Clostridium sp900540255	77.2968	275	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.08	99.08	0.90	0.89	4	-
GCF_002006345.1	s__Clostridium puniceum	76.9116	296	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018223745.1	s__Clostridium beijerinckii	76.8967	255	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.01	95.18	0.85	0.79	244	-
GCF_000621745.1	s__Clostridium beijerinckii_A	76.8576	243	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018917145.1	s__Clostridium_AN bornimense_A	76.4427	176	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956695.1	s__Poseidonibacter parvus	74.651	76	1081	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	98.33	98.33	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:21,872] [INFO] GTDB search result was written to GCF_002050515.1_ASM205051v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:21,873] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:21,878] [INFO] DFAST_QC result json was written to GCF_002050515.1_ASM205051v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:21,878] [INFO] DFAST_QC completed!
[2024-01-24 13:58:21,878] [INFO] Total running time: 0h1m6s