[2024-01-24 13:41:26,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:26,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:26,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ade92d6-27c3-4fef-b5b4-203c73dc992e/dqc_reference
[2024-01-24 13:41:28,238] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:28,239] [INFO] Task started: Prodigal
[2024-01-24 13:41:28,239] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dde7d3f-7085-4fed-b2ab-b0795869f330/GCF_017873245.1_ASM1787324v1_genomic.fna.gz | prodigal -d GCF_017873245.1_ASM1787324v1_genomic.fna/cds.fna -a GCF_017873245.1_ASM1787324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:34,102] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:34,103] [INFO] Task started: HMMsearch
[2024-01-24 13:41:34,103] [INFO] Running command: hmmsearch --tblout GCF_017873245.1_ASM1787324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ade92d6-27c3-4fef-b5b4-203c73dc992e/dqc_reference/reference_markers.hmm GCF_017873245.1_ASM1787324v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:34,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:34,419] [INFO] Found 6/6 markers.
[2024-01-24 13:41:34,452] [INFO] Query marker FASTA was written to GCF_017873245.1_ASM1787324v1_genomic.fna/markers.fasta
[2024-01-24 13:41:34,452] [INFO] Task started: Blastn
[2024-01-24 13:41:34,452] [INFO] Running command: blastn -query GCF_017873245.1_ASM1787324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ade92d6-27c3-4fef-b5b4-203c73dc992e/dqc_reference/reference_markers.fasta -out GCF_017873245.1_ASM1787324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:35,082] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:35,086] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:35,086] [INFO] Target genome list was writen to GCF_017873245.1_ASM1787324v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:35,094] [INFO] Task started: fastANI
[2024-01-24 13:41:35,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dde7d3f-7085-4fed-b2ab-b0795869f330/GCF_017873245.1_ASM1787324v1_genomic.fna.gz --refList GCF_017873245.1_ASM1787324v1_genomic.fna/target_genomes.txt --output GCF_017873245.1_ASM1787324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:49,497] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:49,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ade92d6-27c3-4fef-b5b4-203c73dc992e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:49,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ade92d6-27c3-4fef-b5b4-203c73dc992e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:49,513] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:49,513] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:49,513] [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 tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	100.0	1271	1273	95	conclusive
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	81.6105	730	1273	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	81.2015	650	1273	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	79.4061	433	1273	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	79.1999	458	1273	95	below_threshold
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	79.1301	464	1273	95	below_threshold
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	78.9165	390	1273	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	77.3097	312	1273	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	77.0733	240	1273	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	76.9928	257	1273	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	76.8628	297	1273	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	76.6956	278	1273	95	below_threshold
Clostridium punense	strain=DSM 28650	GCA_017874425.1	1054297	1054297	type	True	76.4285	119	1273	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_000175595.1	217159	217159	type	True	76.3458	157	1273	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	76.3092	167	1273	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	76.2519	167	1273	95	below_threshold
Clostridium ihumii	strain=AP5	GCA_000612845.1	1470356	1470356	type	True	76.2001	222	1273	95	below_threshold
Clostridium cellulovorans	strain=743B	GCA_000145275.1	1493	1493	type	True	76.1201	155	1273	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:49,515] [INFO] DFAST Taxonomy check result was written to GCF_017873245.1_ASM1787324v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:49,516] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:49,516] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:49,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ade92d6-27c3-4fef-b5b4-203c73dc992e/dqc_reference/checkm_data
[2024-01-24 13:41:49,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:49,557] [INFO] Task started: CheckM
[2024-01-24 13:41:49,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873245.1_ASM1787324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873245.1_ASM1787324v1_genomic.fna/checkm_input GCF_017873245.1_ASM1787324v1_genomic.fna/checkm_result
[2024-01-24 13:42:13,144] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:13,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:13,166] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:13,167] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:13,167] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873245.1_ASM1787324v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:13,168] [INFO] Task started: Blastn
[2024-01-24 13:42:13,168] [INFO] Running command: blastn -query GCF_017873245.1_ASM1787324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ade92d6-27c3-4fef-b5b4-203c73dc992e/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873245.1_ASM1787324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:14,007] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:14,010] [INFO] Selected 10 target genomes.
[2024-01-24 13:42:14,010] [INFO] Target genome list was writen to GCF_017873245.1_ASM1787324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:14,017] [INFO] Task started: fastANI
[2024-01-24 13:42:14,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dde7d3f-7085-4fed-b2ab-b0795869f330/GCF_017873245.1_ASM1787324v1_genomic.fna.gz --refList GCF_017873245.1_ASM1787324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873245.1_ASM1787324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:22,739] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:22,755] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:22,756] [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_017873245.1	s__Clostridium tertium	100.0	1271	1273	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.32	97.37	0.91	0.89	19	conclusive
GCA_017888565.1	s__Clostridium sp017888565	92.8854	1072	1273	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_015550425.1	s__Clostridium sp015550425	90.9809	1020	1273	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_000401215.1	s__Clostridium sartagoforme_A	84.4716	794	1273	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.25	98.25	0.85	0.85	2	-
GCF_900086595.1	s__Clostridium nigeriense	81.5947	732	1273	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.98	98.98	0.91	0.91	2	-
GCF_014836325.1	s__Clostridium sp014836325	81.2085	649	1273	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_900759995.1	s__Clostridium sp900759995	80.9064	560	1273	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.46	98.18	0.80	0.79	3	-
GCF_004794105.1	s__Clostridium sartagoforme_B	80.6	680	1273	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	98.58	0.90	0.90	2	-
GCA_018372555.1	s__Clostridium sp018372555	80.2823	500	1273	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	79.4055	433	1273	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:22,758] [INFO] GTDB search result was written to GCF_017873245.1_ASM1787324v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:22,758] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:22,762] [INFO] DFAST_QC result json was written to GCF_017873245.1_ASM1787324v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:22,762] [INFO] DFAST_QC completed!
[2024-01-24 13:42:22,762] [INFO] Total running time: 0h0m56s