[2024-01-24 13:13:12,491] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:12,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:12,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ea07d12-0145-4d9f-8390-c4c673fb6a2c/dqc_reference
[2024-01-24 13:13:13,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:13,883] [INFO] Task started: Prodigal
[2024-01-24 13:13:13,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ba50d91-1d17-4119-aba5-408988920a2d/GCF_902143515.1_P3545_genomic.fna.gz | prodigal -d GCF_902143515.1_P3545_genomic.fna/cds.fna -a GCF_902143515.1_P3545_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:18,923] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:18,923] [INFO] Task started: HMMsearch
[2024-01-24 13:13:18,924] [INFO] Running command: hmmsearch --tblout GCF_902143515.1_P3545_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ea07d12-0145-4d9f-8390-c4c673fb6a2c/dqc_reference/reference_markers.hmm GCF_902143515.1_P3545_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:19,210] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:19,211] [INFO] Found 6/6 markers.
[2024-01-24 13:13:19,241] [INFO] Query marker FASTA was written to GCF_902143515.1_P3545_genomic.fna/markers.fasta
[2024-01-24 13:13:19,241] [INFO] Task started: Blastn
[2024-01-24 13:13:19,241] [INFO] Running command: blastn -query GCF_902143515.1_P3545_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ea07d12-0145-4d9f-8390-c4c673fb6a2c/dqc_reference/reference_markers.fasta -out GCF_902143515.1_P3545_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:19,925] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:19,928] [INFO] Selected 13 target genomes.
[2024-01-24 13:13:19,928] [INFO] Target genome list was writen to GCF_902143515.1_P3545_genomic.fna/target_genomes.txt
[2024-01-24 13:13:20,227] [INFO] Task started: fastANI
[2024-01-24 13:13:20,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ba50d91-1d17-4119-aba5-408988920a2d/GCF_902143515.1_P3545_genomic.fna.gz --refList GCF_902143515.1_P3545_genomic.fna/target_genomes.txt --output GCF_902143515.1_P3545_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:28,704] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:28,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ea07d12-0145-4d9f-8390-c4c673fb6a2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:28,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ea07d12-0145-4d9f-8390-c4c673fb6a2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:28,716] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:28,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:28,717] [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
Hathewaya massiliensis	strain=Marseille-P3545	GCA_902143515.1	1964382	1964382	type	True	100.0	1012	1013	95	conclusive
Hathewaya histolytica	strain=NCTC503	GCA_901482605.1	1498	1498	type	True	80.3584	489	1013	95	below_threshold
Haloimpatiens massiliensis	strain=Mt13	GCA_900184255.1	1658110	1658110	type	True	78.5744	183	1013	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	77.254	149	1013	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	77.161	160	1013	95	below_threshold
Clostridium collagenovorans	strain=DSM 3089	GCA_900130005.1	29357	29357	type	True	77.0005	183	1013	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.579	137	1013	95	below_threshold
Clostridium ihumii	strain=AP5	GCA_000612845.1	1470356	1470356	type	True	76.5307	179	1013	95	below_threshold
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	76.4878	159	1013	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	76.4418	107	1013	95	below_threshold
Clostridium senegalense	strain=type strain: JC122	GCA_000285575.1	1465809	1465809	type	True	76.412	171	1013	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	76.3958	145	1013	95	below_threshold
Clostridium intestinale	strain=DSM 6191	GCA_900130055.1	36845	36845	type	True	76.1206	113	1013	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:28,719] [INFO] DFAST Taxonomy check result was written to GCF_902143515.1_P3545_genomic.fna/tc_result.tsv
[2024-01-24 13:13:28,719] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:28,719] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:28,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ea07d12-0145-4d9f-8390-c4c673fb6a2c/dqc_reference/checkm_data
[2024-01-24 13:13:28,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:28,761] [INFO] Task started: CheckM
[2024-01-24 13:13:28,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902143515.1_P3545_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902143515.1_P3545_genomic.fna/checkm_input GCF_902143515.1_P3545_genomic.fna/checkm_result
[2024-01-24 13:13:50,143] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:50,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:50,168] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:50,168] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:50,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902143515.1_P3545_genomic.fna/markers.fasta)
[2024-01-24 13:13:50,169] [INFO] Task started: Blastn
[2024-01-24 13:13:50,169] [INFO] Running command: blastn -query GCF_902143515.1_P3545_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ea07d12-0145-4d9f-8390-c4c673fb6a2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_902143515.1_P3545_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:51,203] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:51,206] [INFO] Selected 16 target genomes.
[2024-01-24 13:13:51,206] [INFO] Target genome list was writen to GCF_902143515.1_P3545_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:51,264] [INFO] Task started: fastANI
[2024-01-24 13:13:51,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ba50d91-1d17-4119-aba5-408988920a2d/GCF_902143515.1_P3545_genomic.fna.gz --refList GCF_902143515.1_P3545_genomic.fna/target_genomes_gtdb.txt --output GCF_902143515.1_P3545_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:01,857] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:01,870] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:01,871] [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_902143515.1	s__Hathewaya massiliensis	100.0	1012	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_901482605.1	s__Hathewaya histolytica	80.3992	488	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003288255.1	s__Hathewaya sp003288255	79.144	312	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184255.1	s__Haloimpatiens massiliensis	78.6981	184	1013	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_002327185.1	s__Clostridium chauvoei	77.5203	139	1013	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_014836835.1	s__Clostridium_J sp900547625	77.1617	161	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.59	99.59	0.89	0.87	3	-
GCF_900130005.1	s__Clostridium_D collagenovorans	77.0141	182	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000816675.1	s__Clostridium_J argentinense	76.8552	155	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.28	97.50	0.97	0.91	8	-
GCA_002341865.1	s__Clostridium_J sp002341865	76.5875	157	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000619945.1	s__Clostridium_AO lundense	76.549	157	1013	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_000612845.1	s__Clostridium_J ihumii	76.5303	179	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900290265.1	s__Clostridium cagae	76.4418	107	1013	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_900129365.1	s__Clostridium_AH fallax	76.4254	143	1013	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_000285575.1	s__Clostridium_J senegalense	76.4238	170	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	97.19	95.52	0.93	0.91	5	-
GCF_015667795.1	s__Clostridium sp015667795	75.7329	122	1013	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_000498355.1	s__Clostridium sp000498355	75.6097	129	1013	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 13:14:01,872] [INFO] GTDB search result was written to GCF_902143515.1_P3545_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:01,873] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:01,876] [INFO] DFAST_QC result json was written to GCF_902143515.1_P3545_genomic.fna/dqc_result.json
[2024-01-24 13:14:01,876] [INFO] DFAST_QC completed!
[2024-01-24 13:14:01,877] [INFO] Total running time: 0h0m49s