[2024-01-25 19:01:50,790] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:50,792] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:50,792] [INFO] DQC Reference Directory: /var/lib/cwl/stgabe25cf7-ba86-422c-abdc-3f6061b21b9a/dqc_reference
[2024-01-25 19:01:51,976] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:51,977] [INFO] Task started: Prodigal
[2024-01-25 19:01:51,977] [INFO] Running command: gunzip -c /var/lib/cwl/stge595b1bd-13c8-49e6-baa3-2c777936234e/GCF_000320405.1_ASM32040v1_genomic.fna.gz | prodigal -d GCF_000320405.1_ASM32040v1_genomic.fna/cds.fna -a GCF_000320405.1_ASM32040v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:56,216] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:56,216] [INFO] Task started: HMMsearch
[2024-01-25 19:01:56,216] [INFO] Running command: hmmsearch --tblout GCF_000320405.1_ASM32040v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabe25cf7-ba86-422c-abdc-3f6061b21b9a/dqc_reference/reference_markers.hmm GCF_000320405.1_ASM32040v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:56,462] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:56,463] [INFO] Found 6/6 markers.
[2024-01-25 19:01:56,490] [INFO] Query marker FASTA was written to GCF_000320405.1_ASM32040v1_genomic.fna/markers.fasta
[2024-01-25 19:01:56,490] [INFO] Task started: Blastn
[2024-01-25 19:01:56,490] [INFO] Running command: blastn -query GCF_000320405.1_ASM32040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabe25cf7-ba86-422c-abdc-3f6061b21b9a/dqc_reference/reference_markers.fasta -out GCF_000320405.1_ASM32040v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:57,062] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:57,066] [INFO] Selected 28 target genomes.
[2024-01-25 19:01:57,066] [INFO] Target genome list was writen to GCF_000320405.1_ASM32040v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:57,082] [INFO] Task started: fastANI
[2024-01-25 19:01:57,082] [INFO] Running command: fastANI --query /var/lib/cwl/stge595b1bd-13c8-49e6-baa3-2c777936234e/GCF_000320405.1_ASM32040v1_genomic.fna.gz --refList GCF_000320405.1_ASM32040v1_genomic.fna/target_genomes.txt --output GCF_000320405.1_ASM32040v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:14,583] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:14,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabe25cf7-ba86-422c-abdc-3f6061b21b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:14,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabe25cf7-ba86-422c-abdc-3f6061b21b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:14,598] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:02:14,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:14,598] [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	100.0	1119	1126	95	conclusive
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	82.4111	647	1126	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	78.4132	325	1126	95	below_threshold
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	78.4127	326	1126	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	78.4082	306	1126	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	78.2977	319	1126	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	78.1814	308	1126	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	78.0603	341	1126	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	77.423	259	1126	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	77.4034	258	1126	95	below_threshold
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	77.2406	206	1126	95	below_threshold
Clostridium butyricum	strain=NBRC 13949	GCA_007992895.1	1492	1492	type	True	77.1957	232	1126	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.1895	210	1126	95	below_threshold
Clostridium gasigenes	strain=DSM 12272	GCA_900104115.1	94869	94869	type	True	77.1844	285	1126	95	below_threshold
Clostridium butyricum	strain=DSM 10702	GCA_000409755.1	1492	1492	type	True	77.1739	230	1126	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	77.1003	260	1126	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	77.0798	276	1126	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	76.922	253	1126	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	76.8321	216	1126	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	75.7646	121	1126	95	below_threshold
Clostridium arbusti	strain=SL206	GCA_000246895.2	1137848	1137848	type	True	75.7384	101	1126	95	below_threshold
Clostridium pascui	strain=DSM 10365	GCA_016908015.1	46609	46609	type	True	75.7134	102	1126	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	75.6696	156	1126	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	75.6307	151	1126	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:14,600] [INFO] DFAST Taxonomy check result was written to GCF_000320405.1_ASM32040v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:14,600] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:14,600] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:14,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabe25cf7-ba86-422c-abdc-3f6061b21b9a/dqc_reference/checkm_data
[2024-01-25 19:02:14,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:14,638] [INFO] Task started: CheckM
[2024-01-25 19:02:14,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000320405.1_ASM32040v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000320405.1_ASM32040v1_genomic.fna/checkm_input GCF_000320405.1_ASM32040v1_genomic.fna/checkm_result
[2024-01-25 19:02:32,894] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:32,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:32,911] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:32,911] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:32,912] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000320405.1_ASM32040v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:32,912] [INFO] Task started: Blastn
[2024-01-25 19:02:32,912] [INFO] Running command: blastn -query GCF_000320405.1_ASM32040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabe25cf7-ba86-422c-abdc-3f6061b21b9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000320405.1_ASM32040v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:33,738] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:33,740] [INFO] Selected 16 target genomes.
[2024-01-25 19:02:33,741] [INFO] Target genome list was writen to GCF_000320405.1_ASM32040v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:33,757] [INFO] Task started: fastANI
[2024-01-25 19:02:33,757] [INFO] Running command: fastANI --query /var/lib/cwl/stge595b1bd-13c8-49e6-baa3-2c777936234e/GCF_000320405.1_ASM32040v1_genomic.fna.gz --refList GCF_000320405.1_ASM32040v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000320405.1_ASM32040v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:44,949] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:44,959] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:02:44,960] [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_000320405.1	s__Clostridium celatum	100.0	1119	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.74	99.48	0.95	0.91	3	conclusive
GCA_900547475.1	s__Clostridium sp900547475	82.5789	603	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.47	95.30	0.88	0.84	3	-
GCF_000577815.1	s__Clostridium saudiense	82.4603	643	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.39	99.24	0.89	0.87	14	-
GCA_900543325.1	s__Clostridium sp900543325	82.4152	590	1126	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	82.4095	637	1126	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_004353185.1	s__Clostridium cuniculi	82.4012	671	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.75	97.60	0.86	0.82	5	-
GCA_900766315.1	s__Clostridium sp900766315	82.3877	669	1126	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_015670405.1	s__Clostridium sp015670405	82.2147	611	1126	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_910588715.1	s__Clostridium sp910588715	82.0103	535	1126	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_015667795.1	s__Clostridium sp015667795	81.9547	696	1126	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	81.9386	515	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.08	99.08	0.90	0.89	4	-
GCA_017383505.1	s__Clostridium sp017383505	81.6388	314	1126	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_000753455.2	s__Clostridium sp000753455	79.6743	441	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.13	99.13	0.91	0.91	2	-
GCA_000435835.1	s__Clostridium sp000435835	78.7797	356	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.44	99.22	0.92	0.88	4	-
GCF_017873245.1	s__Clostridium tertium	78.0496	342	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.32	97.37	0.91	0.89	19	-
GCA_017888565.1	s__Clostridium sp017888565	78.0467	340	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:44,961] [INFO] GTDB search result was written to GCF_000320405.1_ASM32040v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:44,962] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:44,966] [INFO] DFAST_QC result json was written to GCF_000320405.1_ASM32040v1_genomic.fna/dqc_result.json
[2024-01-25 19:02:44,966] [INFO] DFAST_QC completed!
[2024-01-25 19:02:44,966] [INFO] Total running time: 0h0m54s