[2024-01-24 13:12:56,124] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:56,127] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:56,127] [INFO] DQC Reference Directory: /var/lib/cwl/stgce117f5d-9695-4455-8d4a-c6e4cd13a15c/dqc_reference
[2024-01-24 13:12:57,512] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,514] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,514] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d63cc59-f7fe-47a2-a66e-599d1d5218bf/GCF_026735165.1_ASM2673516v1_genomic.fna.gz | prodigal -d GCF_026735165.1_ASM2673516v1_genomic.fna/cds.fna -a GCF_026735165.1_ASM2673516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:04,094] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:04,095] [INFO] Task started: HMMsearch
[2024-01-24 13:13:04,095] [INFO] Running command: hmmsearch --tblout GCF_026735165.1_ASM2673516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce117f5d-9695-4455-8d4a-c6e4cd13a15c/dqc_reference/reference_markers.hmm GCF_026735165.1_ASM2673516v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:04,429] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:04,431] [INFO] Found 6/6 markers.
[2024-01-24 13:13:04,476] [INFO] Query marker FASTA was written to GCF_026735165.1_ASM2673516v1_genomic.fna/markers.fasta
[2024-01-24 13:13:04,477] [INFO] Task started: Blastn
[2024-01-24 13:13:04,477] [INFO] Running command: blastn -query GCF_026735165.1_ASM2673516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce117f5d-9695-4455-8d4a-c6e4cd13a15c/dqc_reference/reference_markers.fasta -out GCF_026735165.1_ASM2673516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:05,162] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:05,167] [INFO] Selected 40 target genomes.
[2024-01-24 13:13:05,168] [INFO] Target genome list was writen to GCF_026735165.1_ASM2673516v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:05,232] [INFO] Task started: fastANI
[2024-01-24 13:13:05,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d63cc59-f7fe-47a2-a66e-599d1d5218bf/GCF_026735165.1_ASM2673516v1_genomic.fna.gz --refList GCF_026735165.1_ASM2673516v1_genomic.fna/target_genomes.txt --output GCF_026735165.1_ASM2673516v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:27,141] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:27,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce117f5d-9695-4455-8d4a-c6e4cd13a15c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:27,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce117f5d-9695-4455-8d4a-c6e4cd13a15c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:27,165] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:27,165] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:27,165] [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 thermopalmarium	strain=DSM 5974	GCA_002995795.1	29373	29373	suspected-type	True	78.0614	284	1359	95	below_threshold
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	78.0565	320	1359	95	below_threshold
Clostridium thermopalmarium	strain=DSM 5974	GCA_003097175.1	29373	29373	suspected-type	True	77.9613	289	1359	95	below_threshold
Clostridium homopropionicum	strain=DSM 5847	GCA_001263795.1	36844	36844	type	True	77.4072	262	1359	95	below_threshold
Clostridium homopropionicum	strain=DSM 5847	GCA_900113195.1	36844	36844	type	True	77.3798	268	1359	95	below_threshold
Clostridium arbusti	strain=SL206	GCA_000246895.2	1137848	1137848	type	True	76.6882	142	1359	95	below_threshold
Clostridium pascui	strain=DSM 10365	GCA_016908015.1	46609	46609	type	True	76.5947	188	1359	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	76.563	234	1359	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	76.5226	225	1359	95	below_threshold
Clostridium drakei	strain=SL1	GCA_000633595.2	332101	332101	type	True	76.4623	226	1359	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	76.4619	141	1359	95	below_threshold
Clostridium fermenticellae	strain=JN500901	GCA_003600355.1	2068654	2068654	type	True	76.4519	107	1359	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.3768	177	1359	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.3497	160	1359	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	76.3369	199	1359	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	76.305	179	1359	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	76.2906	171	1359	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	76.2761	174	1359	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.1868	185	1359	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	76.1689	155	1359	95	below_threshold
Clostridium algoriphilum	strain=DSM 16153	GCA_020443705.1	198347	198347	type	True	76.1632	145	1359	95	below_threshold
Hathewaya massiliensis	strain=Marseille-P3545	GCA_902143515.1	1964382	1964382	type	True	76.1571	144	1359	95	below_threshold
Clostridium senegalense	strain=type strain: JC122	GCA_000285575.1	1465809	1465809	type	True	76.1459	192	1359	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	76.1375	173	1359	95	below_threshold
Clostridium lacusfryxellense	strain=DSM 14205	GCA_018861735.1	205328	205328	type	True	76.1254	169	1359	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	76.1241	161	1359	95	below_threshold
Tepidibacter thalassicus	strain=DSM 15285	GCA_900129915.1	214905	214905	type	True	75.8606	103	1359	95	below_threshold
Tissierella pigra	strain=WCA3-693-APC-4	GCA_009695605.1	2607614	2607614	type	True	75.2101	73	1359	95	below_threshold
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	74.6871	57	1359	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	74.6819	58	1359	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:27,167] [INFO] DFAST Taxonomy check result was written to GCF_026735165.1_ASM2673516v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:27,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:27,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:27,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce117f5d-9695-4455-8d4a-c6e4cd13a15c/dqc_reference/checkm_data
[2024-01-24 13:13:27,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:27,215] [INFO] Task started: CheckM
[2024-01-24 13:13:27,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026735165.1_ASM2673516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026735165.1_ASM2673516v1_genomic.fna/checkm_input GCF_026735165.1_ASM2673516v1_genomic.fna/checkm_result
[2024-01-24 13:13:55,619] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:55,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:55,638] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:55,638] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:55,638] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026735165.1_ASM2673516v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:55,639] [INFO] Task started: Blastn
[2024-01-24 13:13:55,639] [INFO] Running command: blastn -query GCF_026735165.1_ASM2673516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce117f5d-9695-4455-8d4a-c6e4cd13a15c/dqc_reference/reference_markers_gtdb.fasta -out GCF_026735165.1_ASM2673516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:56,437] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:56,440] [INFO] Selected 28 target genomes.
[2024-01-24 13:13:56,441] [INFO] Target genome list was writen to GCF_026735165.1_ASM2673516v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:56,464] [INFO] Task started: fastANI
[2024-01-24 13:13:56,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d63cc59-f7fe-47a2-a66e-599d1d5218bf/GCF_026735165.1_ASM2673516v1_genomic.fna.gz --refList GCF_026735165.1_ASM2673516v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026735165.1_ASM2673516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:11,724] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:11,747] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:14:11,748] [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_003614235.1	s__Clostridium_H haemolyticum	78.4516	307	1359	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_000204565.1	s__Clostridium_H botulinum_B	78.2672	325	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0162	99.87	99.52	0.98	0.95	19	-
GCA_009738435.1	s__Clostridium_H bovifaecis	78.1449	329	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017100085.1	s__Clostridium_H botulinum_A	78.1385	325	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0162	99.30	99.03	0.94	0.90	14	-
GCF_000014125.1	s__Clostridium_H novyi	78.1139	298	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.92	96.35	0.94	0.92	7	-
GCF_900176615.1	s__Clostridium_H massiliodielmoense	78.0668	322	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.64	96.44	0.92	0.87	5	-
GCF_002995795.1	s__Clostridium_H thermopalmarium	78.0394	288	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	99.57	99.32	0.95	0.92	4	-
GCF_001263795.1	s__Clostridium_H homopropionicum	77.4302	260	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900185645.1	s__Clostridium_AK sp900185645	76.9155	177	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	96.24	95.22	0.84	0.82	3	-
GCF_003718715.1	s__JN-1 sp003718715	76.891	127	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__JN-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001243045.1	s__Clostridium_F niameyense	76.7602	201	1359	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	-
GCF_000246895.1	s__Clostridium_I arbusti	76.6732	143	1359	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	-
GCF_000968375.1	s__Clostridium_AM scatologenes	76.6125	241	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	N/A	N/A	N/A	N/A	1	-
GCF_016908015.1	s__Clostridium_AK pascui	76.5855	189	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633595.2	s__Clostridium_AM drakei	76.4714	225	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	100.00	100.00	1.00	1.00	2	-
GCF_014287815.1	s__Clostridium sp001916075	76.4672	140	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.32	99.07	0.94	0.92	6	-
GCF_003600355.1	s__JN-1 sp003600355	76.4349	108	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__JN-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000816675.1	s__Clostridium_J argentinense	76.4027	191	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.28	97.50	0.97	0.91	8	-
GCF_000424205.1	s__Clostridium_X cadaveris	76.2459	105	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_X	95.0	99.52	99.40	0.92	0.82	7	-
GCF_014836835.1	s__Clostridium_J sp900547625	76.1965	184	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.59	99.59	0.89	0.87	3	-
GCF_902143515.1	s__Hathewaya massiliensis	76.1339	142	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000435835.1	s__Clostridium sp000435835	75.9182	131	1359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.44	99.22	0.92	0.88	4	-
GCA_015058405.1	s__Clostridium sp015058405	75.8971	127	1359	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 13:14:11,765] [INFO] GTDB search result was written to GCF_026735165.1_ASM2673516v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:11,766] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:11,775] [INFO] DFAST_QC result json was written to GCF_026735165.1_ASM2673516v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:11,775] [INFO] DFAST_QC completed!
[2024-01-24 13:14:11,776] [INFO] Total running time: 0h1m16s