[2024-01-24 11:51:23,829] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:23,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:23,831] [INFO] DQC Reference Directory: /var/lib/cwl/stgcae3a4a2-f48e-4494-b6cc-bf04e59f8209/dqc_reference
[2024-01-24 11:51:25,135] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:25,136] [INFO] Task started: Prodigal
[2024-01-24 11:51:25,137] [INFO] Running command: gunzip -c /var/lib/cwl/stge51c6bec-ed36-41ad-b02e-4e8745095d3c/GCF_014287825.1_ASM1428782v1_genomic.fna.gz | prodigal -d GCF_014287825.1_ASM1428782v1_genomic.fna/cds.fna -a GCF_014287825.1_ASM1428782v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:31,132] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:31,132] [INFO] Task started: HMMsearch
[2024-01-24 11:51:31,132] [INFO] Running command: hmmsearch --tblout GCF_014287825.1_ASM1428782v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcae3a4a2-f48e-4494-b6cc-bf04e59f8209/dqc_reference/reference_markers.hmm GCF_014287825.1_ASM1428782v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:31,453] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:31,454] [INFO] Found 6/6 markers.
[2024-01-24 11:51:31,491] [INFO] Query marker FASTA was written to GCF_014287825.1_ASM1428782v1_genomic.fna/markers.fasta
[2024-01-24 11:51:31,492] [INFO] Task started: Blastn
[2024-01-24 11:51:31,492] [INFO] Running command: blastn -query GCF_014287825.1_ASM1428782v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcae3a4a2-f48e-4494-b6cc-bf04e59f8209/dqc_reference/reference_markers.fasta -out GCF_014287825.1_ASM1428782v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:32,091] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:32,095] [INFO] Selected 26 target genomes.
[2024-01-24 11:51:32,095] [INFO] Target genome list was writen to GCF_014287825.1_ASM1428782v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:32,125] [INFO] Task started: fastANI
[2024-01-24 11:51:32,126] [INFO] Running command: fastANI --query /var/lib/cwl/stge51c6bec-ed36-41ad-b02e-4e8745095d3c/GCF_014287825.1_ASM1428782v1_genomic.fna.gz --refList GCF_014287825.1_ASM1428782v1_genomic.fna/target_genomes.txt --output GCF_014287825.1_ASM1428782v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:48,885] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:48,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcae3a4a2-f48e-4494-b6cc-bf04e59f8209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:48,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcae3a4a2-f48e-4494-b6cc-bf04e59f8209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:48,905] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:48,905] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:48,906] [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 celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	79.7437	439	1361	95	below_threshold
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	79.7148	439	1361	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	78.237	311	1361	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	78.2232	308	1361	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	78.1881	316	1361	95	below_threshold
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	78.186	315	1361	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	78.1827	316	1361	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	77.4484	236	1361	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	77.3569	203	1361	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	77.2376	203	1361	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	77.1134	240	1361	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	77.0732	232	1361	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	76.6385	215	1361	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.6106	117	1361	95	below_threshold
Clostridium putrefaciens	strain=NCTC9836	GCA_900461105.1	99675	99675	type	True	76.2468	90	1361	95	below_threshold
Clostridium liquoris	strain=DSM 100320	GCA_002995785.1	1289519	1289519	type	True	76.1191	74	1361	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	76.0158	151	1361	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	75.9446	144	1361	95	below_threshold
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	75.9372	143	1361	95	below_threshold
Clostridium arbusti	strain=SL206	GCA_000246895.2	1137848	1137848	type	True	75.6889	101	1361	95	below_threshold
Clostridium pasteurianum	strain=ATCC 6013	GCA_001856645.1	1501	1501	type	True	75.4201	121	1361	95	below_threshold
Clostridium pasteurianum	strain=ATCC 6013	GCA_000724205.3	1501	1501	type	True	75.4156	120	1361	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000807255.1	1501	1501	type	True	75.4102	120	1361	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000330945.1	1501	1501	type	True	75.357	121	1361	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:48,908] [INFO] DFAST Taxonomy check result was written to GCF_014287825.1_ASM1428782v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:48,909] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:48,909] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:48,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcae3a4a2-f48e-4494-b6cc-bf04e59f8209/dqc_reference/checkm_data
[2024-01-24 11:51:48,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:48,958] [INFO] Task started: CheckM
[2024-01-24 11:51:48,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287825.1_ASM1428782v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287825.1_ASM1428782v1_genomic.fna/checkm_input GCF_014287825.1_ASM1428782v1_genomic.fna/checkm_result
[2024-01-24 11:52:13,978] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:13,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:14,002] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:14,002] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:14,003] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287825.1_ASM1428782v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:14,003] [INFO] Task started: Blastn
[2024-01-24 11:52:14,003] [INFO] Running command: blastn -query GCF_014287825.1_ASM1428782v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcae3a4a2-f48e-4494-b6cc-bf04e59f8209/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287825.1_ASM1428782v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:14,860] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:14,866] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:14,866] [INFO] Target genome list was writen to GCF_014287825.1_ASM1428782v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:14,899] [INFO] Task started: fastANI
[2024-01-24 11:52:14,900] [INFO] Running command: fastANI --query /var/lib/cwl/stge51c6bec-ed36-41ad-b02e-4e8745095d3c/GCF_014287825.1_ASM1428782v1_genomic.fna.gz --refList GCF_014287825.1_ASM1428782v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287825.1_ASM1428782v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:26,562] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:26,576] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:26,576] [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
GCA_000753455.2	s__Clostridium sp000753455	99.1277	1231	1361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.13	99.13	0.91	0.91	2	conclusive
GCF_001405015.1	s__Clostridium disporicum	87.152	891	1361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.24	98.87	0.93	0.88	4	-
GCF_000320405.1	s__Clostridium celatum	79.7761	435	1361	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_000577815.1	s__Clostridium saudiense	79.7406	436	1361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.39	99.24	0.89	0.87	14	-
GCF_004353185.1	s__Clostridium cuniculi	79.7257	484	1361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.75	97.60	0.86	0.82	5	-
GCF_015670405.1	s__Clostridium sp015670405	79.5549	407	1361	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_900547475.1	s__Clostridium sp900547475	79.5111	424	1361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.47	95.30	0.88	0.84	3	-
GCA_900766315.1	s__Clostridium sp900766315	79.4711	472	1361	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_015555905.1	s__Clostridium sp015555905	79.456	410	1361	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_015667795.1	s__Clostridium sp015667795	79.2295	492	1361	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_900543325.1	s__Clostridium sp900543325	79.1768	396	1361	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_900540255.1	s__Clostridium sp900540255	79.1558	386	1361	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_002327185.1	s__Clostridium chauvoei	78.1977	309	1361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCA_018372875.1	s__Clostridium sp018372875	77.8215	246	1361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.91	98.91	0.87	0.87	2	-
GCA_012520205.1	s__Clostridium sp012520205	77.65	160	1361	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_000619945.1	s__Clostridium_AO lundense	75.9364	141	1361	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_000246895.1	s__Clostridium_I arbusti	75.6779	102	1361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:26,578] [INFO] GTDB search result was written to GCF_014287825.1_ASM1428782v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:26,578] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:26,583] [INFO] DFAST_QC result json was written to GCF_014287825.1_ASM1428782v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:26,583] [INFO] DFAST_QC completed!
[2024-01-24 11:52:26,583] [INFO] Total running time: 0h1m3s