[2024-01-24 12:37:25,199] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:25,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:25,204] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b1c420a-4f28-4941-bfaa-d94a1ef3e0d0/dqc_reference
[2024-01-24 12:37:26,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:26,514] [INFO] Task started: Prodigal
[2024-01-24 12:37:26,514] [INFO] Running command: gunzip -c /var/lib/cwl/stge36e83ac-cb48-45ab-a09b-9aace014aaa7/GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna.gz | prodigal -d GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/cds.fna -a GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:32,066] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:32,066] [INFO] Task started: HMMsearch
[2024-01-24 12:37:32,067] [INFO] Running command: hmmsearch --tblout GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b1c420a-4f28-4941-bfaa-d94a1ef3e0d0/dqc_reference/reference_markers.hmm GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:32,344] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:32,345] [INFO] Found 6/6 markers.
[2024-01-24 12:37:32,382] [INFO] Query marker FASTA was written to GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/markers.fasta
[2024-01-24 12:37:32,382] [INFO] Task started: Blastn
[2024-01-24 12:37:32,382] [INFO] Running command: blastn -query GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b1c420a-4f28-4941-bfaa-d94a1ef3e0d0/dqc_reference/reference_markers.fasta -out GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:33,004] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:33,007] [INFO] Selected 22 target genomes.
[2024-01-24 12:37:33,008] [INFO] Target genome list was writen to GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:33,016] [INFO] Task started: fastANI
[2024-01-24 12:37:33,016] [INFO] Running command: fastANI --query /var/lib/cwl/stge36e83ac-cb48-45ab-a09b-9aace014aaa7/GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna.gz --refList GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/target_genomes.txt --output GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:46,245] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:46,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b1c420a-4f28-4941-bfaa-d94a1ef3e0d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:46,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b1c420a-4f28-4941-bfaa-d94a1ef3e0d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:46,264] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:46,264] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:46,265] [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 polynesiense	strain=MS1	GCA_000820705.1	1325933	1325933	type	True	100.0	1094	1104	95	conclusive
Clostridium amylolyticum	strain=DSM 21864	GCA_900142075.1	1121298	1121298	type	True	78.9423	354	1104	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	76.8403	65	1104	95	below_threshold
Desnuesiella massiliensis	strain=mt10	GCA_001403615.1	1650662	1650662	type	True	76.7851	130	1104	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	76.7458	83	1104	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.6066	103	1104	95	below_threshold
Clostridium perfringens	strain=ATCC 13124	GCA_000013285.1	1502	1502	type	True	76.4769	78	1104	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	76.4651	68	1104	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	76.3276	108	1104	95	below_threshold
Clostridium perfringens	strain=FDAARGOS_903	GCA_016027375.1	1502	1502	type	True	76.3249	80	1104	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	76.1358	71	1104	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.1151	82	1104	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.1106	87	1104	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	76.0607	64	1104	95	below_threshold
Clostridium ljungdahlii	strain=DSM 13528	GCA_000143685.1	1538	1538	suspected-type	True	76.0425	57	1104	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	75.8791	56	1104	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	75.8579	74	1104	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	75.8558	78	1104	95	below_threshold
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	75.7503	73	1104	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000427255.1	84023	84023	suspected-type	True	75.487	54	1104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:46,266] [INFO] DFAST Taxonomy check result was written to GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:46,267] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:46,267] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:46,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b1c420a-4f28-4941-bfaa-d94a1ef3e0d0/dqc_reference/checkm_data
[2024-01-24 12:37:46,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:46,303] [INFO] Task started: CheckM
[2024-01-24 12:37:46,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/checkm_input GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/checkm_result
[2024-01-24 12:38:09,592] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:09,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:09,611] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:09,612] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:09,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/markers.fasta)
[2024-01-24 12:38:09,613] [INFO] Task started: Blastn
[2024-01-24 12:38:09,613] [INFO] Running command: blastn -query GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b1c420a-4f28-4941-bfaa-d94a1ef3e0d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:10,577] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:10,580] [INFO] Selected 23 target genomes.
[2024-01-24 12:38:10,580] [INFO] Target genome list was writen to GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:10,603] [INFO] Task started: fastANI
[2024-01-24 12:38:10,604] [INFO] Running command: fastANI --query /var/lib/cwl/stge36e83ac-cb48-45ab-a09b-9aace014aaa7/GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna.gz --refList GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/target_genomes_gtdb.txt --output GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:24,142] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:24,158] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:24,159] [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_000820705.1	s__Clostridium_AA polynesiense	100.0	1094	1104	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AA	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_900142075.1	s__Clostridium_AA amylolyticum	78.9495	353	1104	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AA	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002327185.1	s__Clostridium chauvoei	76.927	66	1104	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_003606265.1	s__Clostridium septicum	76.8652	75	1104	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.65	99.48	0.94	0.92	5	-
GCF_001403615.1	s__Desnuesiella massiliensis	76.8029	129	1104	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Desnuesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000753435.1	s__Clostridium_L amazonitimonense	76.5967	106	1104	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	76.4945	67	1104	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_000013285.1	s__Clostridium_P perfringens	76.4501	79	1104	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.05	95.74	0.91	0.81	315	-
GCF_016765615.1	s__Clostridium_T sp016765615	76.4286	63	1104	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	-
GCF_004794105.1	s__Clostridium sartagoforme_B	76.3977	69	1104	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_002298125.1	s__UBA701 sp002298125	76.3436	51	1104	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__UBA701	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595795.1	s__Clostridium_AR sp016595795	76.3353	79	1104	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765585.1	s__F0540 sp016765585	76.3201	94	1104	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017888565.1	s__Clostridium sp017888565	76.3186	81	1104	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_007115085.1	s__Clostridium sp007115085	76.1276	68	1104	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.42	99.42	0.90	0.90	2	-
GCF_000744935.1	s__Haloimpatiens sp000744935	76.1178	74	1104	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_000143685.1	s__Clostridium_B ljungdahlii	76.0176	58	1104	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	98.76	97.79	0.92	0.88	9	-
GCF_004006395.2	s__Clostridium_B sp004006395	75.9176	58	1104	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019207025.1	s__Clostridium_AM sp019207025	75.8579	74	1104	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001243045.1	s__Clostridium_F niameyense	75.7723	74	1104	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.56	99.11	0.96	0.92	3	-
GCA_018372555.1	s__Clostridium sp018372555	75.7405	55	1104	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 12:38:24,160] [INFO] GTDB search result was written to GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:24,161] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:24,165] [INFO] DFAST_QC result json was written to GCF_000820705.1_Clostridium_polynesiense_str._MS1_genomic.fna/dqc_result.json
[2024-01-24 12:38:24,165] [INFO] DFAST_QC completed!
[2024-01-24 12:38:24,165] [INFO] Total running time: 0h0m59s