[2024-01-24 13:08:58,475] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:58,476] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:58,476] [INFO] DQC Reference Directory: /var/lib/cwl/stg882bd431-b2f7-4096-a683-5e4145e3189e/dqc_reference
[2024-01-24 13:08:59,756] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,757] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,758] [INFO] Running command: gunzip -c /var/lib/cwl/stg4cd74ae1-c975-413a-905a-d734fd4778ec/GCF_000577895.1_M2_40_genomic.fna.gz | prodigal -d GCF_000577895.1_M2_40_genomic.fna/cds.fna -a GCF_000577895.1_M2_40_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:05,433] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:05,433] [INFO] Task started: HMMsearch
[2024-01-24 13:09:05,433] [INFO] Running command: hmmsearch --tblout GCF_000577895.1_M2_40_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg882bd431-b2f7-4096-a683-5e4145e3189e/dqc_reference/reference_markers.hmm GCF_000577895.1_M2_40_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:05,737] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:05,739] [INFO] Found 6/6 markers.
[2024-01-24 13:09:05,770] [INFO] Query marker FASTA was written to GCF_000577895.1_M2_40_genomic.fna/markers.fasta
[2024-01-24 13:09:05,771] [INFO] Task started: Blastn
[2024-01-24 13:09:05,771] [INFO] Running command: blastn -query GCF_000577895.1_M2_40_genomic.fna/markers.fasta -db /var/lib/cwl/stg882bd431-b2f7-4096-a683-5e4145e3189e/dqc_reference/reference_markers.fasta -out GCF_000577895.1_M2_40_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:06,360] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:06,364] [INFO] Selected 29 target genomes.
[2024-01-24 13:09:06,365] [INFO] Target genome list was writen to GCF_000577895.1_M2_40_genomic.fna/target_genomes.txt
[2024-01-24 13:09:06,520] [INFO] Task started: fastANI
[2024-01-24 13:09:06,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cd74ae1-c975-413a-905a-d734fd4778ec/GCF_000577895.1_M2_40_genomic.fna.gz --refList GCF_000577895.1_M2_40_genomic.fna/target_genomes.txt --output GCF_000577895.1_M2_40_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:22,773] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:22,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg882bd431-b2f7-4096-a683-5e4145e3189e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:22,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg882bd431-b2f7-4096-a683-5e4145e3189e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:22,801] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:22,802] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:22,802] [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 bornimense	strain=type strain: M2/40	GCA_000577895.1	1216932	1216932	type	True	100.0	1202	1205	95	conclusive
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	77.9023	169	1205	95	below_threshold
Clostridium cellulovorans	strain=743B	GCA_000145275.1	1493	1493	type	True	77.7301	172	1205	95	below_threshold
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	77.6305	142	1205	95	below_threshold
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	77.5504	119	1205	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	77.5237	141	1205	95	below_threshold
Clostridium perfringens	strain=ATCC 13124	GCA_000013285.1	1502	1502	type	True	77.3068	150	1205	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	77.2487	157	1205	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	76.988	154	1205	95	below_threshold
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	76.7394	169	1205	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	76.7078	177	1205	95	below_threshold
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	76.5931	139	1205	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	76.3537	162	1205	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	76.2365	103	1205	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.2222	111	1205	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_011017965.1	1491	1491	type	True	76.2152	147	1205	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.2108	190	1205	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.206	147	1205	95	below_threshold
Clostridium senegalense	strain=type strain: JC122	GCA_000285575.1	1465809	1465809	type	True	76.1869	148	1205	95	below_threshold
Clostridium acetireducens	strain=DSM 10703	GCA_001758365.1	76489	76489	type	True	76.1721	126	1205	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_001276985.1	1491	1491	type	True	76.158	151	1205	95	below_threshold
Clostridium tepidiprofundi	strain=DSM 19306	GCA_001594005.1	420412	420412	type	True	75.8469	86	1205	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	75.7864	127	1205	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:22,804] [INFO] DFAST Taxonomy check result was written to GCF_000577895.1_M2_40_genomic.fna/tc_result.tsv
[2024-01-24 13:09:22,804] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:22,804] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:22,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg882bd431-b2f7-4096-a683-5e4145e3189e/dqc_reference/checkm_data
[2024-01-24 13:09:22,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:22,842] [INFO] Task started: CheckM
[2024-01-24 13:09:22,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000577895.1_M2_40_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000577895.1_M2_40_genomic.fna/checkm_input GCF_000577895.1_M2_40_genomic.fna/checkm_result
[2024-01-24 13:09:46,500] [INFO] Task succeeded: CheckM
[2024-01-24 13:09:46,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:09:46,521] [INFO] ===== Completeness check finished =====
[2024-01-24 13:09:46,521] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:09:46,522] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000577895.1_M2_40_genomic.fna/markers.fasta)
[2024-01-24 13:09:46,522] [INFO] Task started: Blastn
[2024-01-24 13:09:46,522] [INFO] Running command: blastn -query GCF_000577895.1_M2_40_genomic.fna/markers.fasta -db /var/lib/cwl/stg882bd431-b2f7-4096-a683-5e4145e3189e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000577895.1_M2_40_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:47,389] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:47,393] [INFO] Selected 23 target genomes.
[2024-01-24 13:09:47,393] [INFO] Target genome list was writen to GCF_000577895.1_M2_40_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:09:47,542] [INFO] Task started: fastANI
[2024-01-24 13:09:47,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cd74ae1-c975-413a-905a-d734fd4778ec/GCF_000577895.1_M2_40_genomic.fna.gz --refList GCF_000577895.1_M2_40_genomic.fna/target_genomes_gtdb.txt --output GCF_000577895.1_M2_40_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:02,120] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:02,143] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:02,143] [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_000577895.1	s__Clostridium_AN bornimense	100.0	1202	1205	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	conclusive
GCF_018917145.1	s__Clostridium_AN bornimense_A	88.1235	886	1205	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_900447045.1	s__Clostridium paraputrificum	77.9132	169	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.58	95.42	0.89	0.83	29	-
GCF_002285495.1	s__Clostridium isatidis	77.5271	141	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.19	99.19	0.81	0.81	2	-
GCA_000753435.1	s__Clostridium_L amazonitimonense	77.4923	118	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	99.33	97.98	0.97	0.93	4	-
GCF_900456775.1	s__Clostridium_P ventriculi	77.4334	139	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.93	98.34	0.95	0.94	8	-
GCF_006742065.1	s__Clostridium butyricum	77.296	189	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	97.46	0.89	0.80	64	-
GCF_002050515.1	s__Clostridium thermobutyricum	76.7108	179	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.10	97.10	0.91	0.89	3	-
GCF_900129365.1	s__Clostridium_AH fallax	76.5401	150	1205	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_000401215.1	s__Clostridium sartagoforme_A	76.3435	172	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.25	98.25	0.85	0.85	2	-
GCA_017888565.1	s__Clostridium sp017888565	76.3078	165	1205	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_018918285.1	s__MSJ-11 sp018918285	76.2365	103	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__MSJ-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000285575.1	s__Clostridium_J senegalense	76.1954	147	1205	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_001276985.1	s__Clostridium_F botulinum	76.1686	150	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.69	95.97	0.92	0.83	213	-
GCF_001758365.1	s__Clostridium_C acetireducens	76.1599	127	1205	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_000612845.1	s__Clostridium_J ihumii	76.0532	170	1205	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_001276215.1	s__Clostridium_F sp001276215	76.017	147	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.32	95.44	0.88	0.82	10	-
GCA_002341865.1	s__Clostridium_J sp002341865	75.9007	124	1205	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_900167505.1	s__F0540 sp900167505	75.8806	126	1205	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	98.87	98.87	0.90	0.90	2	-
GCA_002455975.1	s__Clostridium_J sp002455975	75.8344	124	1205	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:02,146] [INFO] GTDB search result was written to GCF_000577895.1_M2_40_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:02,147] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:02,152] [INFO] DFAST_QC result json was written to GCF_000577895.1_M2_40_genomic.fna/dqc_result.json
[2024-01-24 13:10:02,152] [INFO] DFAST_QC completed!
[2024-01-24 13:10:02,152] [INFO] Total running time: 0h1m4s