[2024-01-25 20:01:05,729] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:01:05,733] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:01:05,733] [INFO] DQC Reference Directory: /var/lib/cwl/stgde6ca31c-5aa3-4cf0-a53f-f751533fb95c/dqc_reference
[2024-01-25 20:01:07,012] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:01:07,013] [INFO] Task started: Prodigal
[2024-01-25 20:01:07,013] [INFO] Running command: gunzip -c /var/lib/cwl/stga6114fdc-852b-4f3d-9491-9fb8247d4b58/GCF_016765615.1_ASM1676561v1_genomic.fna.gz | prodigal -d GCF_016765615.1_ASM1676561v1_genomic.fna/cds.fna -a GCF_016765615.1_ASM1676561v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:12,699] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:12,699] [INFO] Task started: HMMsearch
[2024-01-25 20:01:12,699] [INFO] Running command: hmmsearch --tblout GCF_016765615.1_ASM1676561v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde6ca31c-5aa3-4cf0-a53f-f751533fb95c/dqc_reference/reference_markers.hmm GCF_016765615.1_ASM1676561v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:12,952] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:12,953] [INFO] Found 6/6 markers.
[2024-01-25 20:01:12,986] [INFO] Query marker FASTA was written to GCF_016765615.1_ASM1676561v1_genomic.fna/markers.fasta
[2024-01-25 20:01:12,986] [INFO] Task started: Blastn
[2024-01-25 20:01:12,987] [INFO] Running command: blastn -query GCF_016765615.1_ASM1676561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde6ca31c-5aa3-4cf0-a53f-f751533fb95c/dqc_reference/reference_markers.fasta -out GCF_016765615.1_ASM1676561v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:13,546] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:13,549] [INFO] Selected 26 target genomes.
[2024-01-25 20:01:13,549] [INFO] Target genome list was writen to GCF_016765615.1_ASM1676561v1_genomic.fna/target_genomes.txt
[2024-01-25 20:01:13,590] [INFO] Task started: fastANI
[2024-01-25 20:01:13,591] [INFO] Running command: fastANI --query /var/lib/cwl/stga6114fdc-852b-4f3d-9491-9fb8247d4b58/GCF_016765615.1_ASM1676561v1_genomic.fna.gz --refList GCF_016765615.1_ASM1676561v1_genomic.fna/target_genomes.txt --output GCF_016765615.1_ASM1676561v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:29,950] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:29,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde6ca31c-5aa3-4cf0-a53f-f751533fb95c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:29,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde6ca31c-5aa3-4cf0-a53f-f751533fb95c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:29,964] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:01:29,965] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:01:29,965] [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 intestinale	strain=DSM 6191	GCA_900130055.1	36845	36845	type	True	78.5465	400	1344	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	77.3966	205	1344	95	below_threshold
Clostridium perfringens	strain=ATCC 13124	GCA_000013285.1	1502	1502	type	True	77.3518	164	1344	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	77.3333	195	1344	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	77.3249	195	1344	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	77.2672	183	1344	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	77.2648	201	1344	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	77.2384	177	1344	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	77.2348	191	1344	95	below_threshold
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	77.2131	163	1344	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	77.1829	177	1344	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	77.1465	215	1344	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	77.1209	188	1344	95	below_threshold
Clostridium sardiniense	strain=DSM 2632	GCA_016907995.1	29369	29369	type	True	77.0836	168	1344	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	77.0742	189	1344	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.0166	185	1344	95	below_threshold
Clostridium neonatale	strain=LCDC no.99-A-005	GCA_001458595.1	137838	137838	type	True	76.9886	191	1344	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	76.9557	181	1344	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	76.9373	250	1344	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	76.8919	188	1344	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	76.6578	155	1344	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.4944	167	1344	95	below_threshold
Clostridium amylolyticum	strain=DSM 21864	GCA_900142075.1	1121298	1121298	type	True	76.4597	136	1344	95	below_threshold
Clostridium grantii	strain=DSM 8605	GCA_900129965.1	40575	40575	type	True	76.091	104	1344	95	below_threshold
Oceanirhabdus seepicola	strain=ZWT	GCA_023684385.1	2828781	2828781	type	True	75.7205	81	1344	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:29,968] [INFO] DFAST Taxonomy check result was written to GCF_016765615.1_ASM1676561v1_genomic.fna/tc_result.tsv
[2024-01-25 20:01:29,968] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:29,968] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:29,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde6ca31c-5aa3-4cf0-a53f-f751533fb95c/dqc_reference/checkm_data
[2024-01-25 20:01:29,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:30,011] [INFO] Task started: CheckM
[2024-01-25 20:01:30,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016765615.1_ASM1676561v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016765615.1_ASM1676561v1_genomic.fna/checkm_input GCF_016765615.1_ASM1676561v1_genomic.fna/checkm_result
[2024-01-25 20:01:52,784] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:52,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:52,802] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:52,802] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:52,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016765615.1_ASM1676561v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:52,803] [INFO] Task started: Blastn
[2024-01-25 20:01:52,803] [INFO] Running command: blastn -query GCF_016765615.1_ASM1676561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde6ca31c-5aa3-4cf0-a53f-f751533fb95c/dqc_reference/reference_markers_gtdb.fasta -out GCF_016765615.1_ASM1676561v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:53,587] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:53,590] [INFO] Selected 23 target genomes.
[2024-01-25 20:01:53,590] [INFO] Target genome list was writen to GCF_016765615.1_ASM1676561v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:53,614] [INFO] Task started: fastANI
[2024-01-25 20:01:53,614] [INFO] Running command: fastANI --query /var/lib/cwl/stga6114fdc-852b-4f3d-9491-9fb8247d4b58/GCF_016765615.1_ASM1676561v1_genomic.fna.gz --refList GCF_016765615.1_ASM1676561v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016765615.1_ASM1676561v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:08,915] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:08,931] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:08,932] [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_016765615.1	s__Clostridium_T sp016765615	100.0	1344	1344	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_T	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900130055.1	s__Clostridium_T intestinale	78.5571	399	1344	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_T	95.0	95.87	95.52	0.87	0.83	4	-
GCF_017873245.1	s__Clostridium tertium	77.3966	205	1344	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.32	97.37	0.91	0.89	19	-
GCF_900086595.1	s__Clostridium nigeriense	77.3623	193	1344	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_900129365.1	s__Clostridium_AH fallax	77.2795	189	1344	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_000498355.1	s__Clostridium sp000498355	77.2697	176	1344	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_002050515.1	s__Clostridium thermobutyricum	77.2642	201	1344	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_000320405.1	s__Clostridium celatum	77.2384	177	1344	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.74	99.48	0.95	0.91	3	-
GCF_002285495.1	s__Clostridium isatidis	77.2126	163	1344	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_900759995.1	s__Clostridium sp900759995	77.1573	181	1344	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_009295725.1	s__Clostridium_P tarantellae	77.1059	189	1344	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907995.1	s__Clostridium sardiniense	77.0993	167	1344	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_900290265.1	s__Clostridium cagae	77.0897	204	1344	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_000621745.1	s__Clostridium beijerinckii_A	77.0721	212	1344	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_017888565.1	s__Clostridium sp017888565	77.01	208	1344	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_001458595.1	s__Clostridium neonatale	77.0019	190	1344	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.07	98.42	0.91	0.80	11	-
GCF_001403635.1	s__Clostridium_P massiliamazoniense	76.9518	179	1344	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900141845.1	s__Clostridium_AG cavendishii	76.9486	249	1344	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AG	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827935.1	s__Clostridium botulinum_A	76.9113	207	1344	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_012519155.1	s__Clostridium sp012519155	76.7198	112	1344	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_003614235.1	s__Clostridium_H haemolyticum	76.4198	129	1344	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.44	97.38	0.90	0.84	13	-
GCF_900129965.1	s__Clostridium_AF grantii	76.091	104	1344	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AF	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:08,934] [INFO] GTDB search result was written to GCF_016765615.1_ASM1676561v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:08,934] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:08,938] [INFO] DFAST_QC result json was written to GCF_016765615.1_ASM1676561v1_genomic.fna/dqc_result.json
[2024-01-25 20:02:08,938] [INFO] DFAST_QC completed!
[2024-01-25 20:02:08,938] [INFO] Total running time: 0h1m3s