[2024-01-24 11:05:28,085] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:28,087] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:28,087] [INFO] DQC Reference Directory: /var/lib/cwl/stg8365a78a-a8de-42fe-8d02-ab0d189f4cd4/dqc_reference
[2024-01-24 11:05:29,437] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,441] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,441] [INFO] Running command: gunzip -c /var/lib/cwl/stg499367ec-7485-42e0-93e0-d47c91cb527d/GCF_016908015.1_ASM1690801v1_genomic.fna.gz | prodigal -d GCF_016908015.1_ASM1690801v1_genomic.fna/cds.fna -a GCF_016908015.1_ASM1690801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:36,025] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:36,026] [INFO] Task started: HMMsearch
[2024-01-24 11:05:36,026] [INFO] Running command: hmmsearch --tblout GCF_016908015.1_ASM1690801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8365a78a-a8de-42fe-8d02-ab0d189f4cd4/dqc_reference/reference_markers.hmm GCF_016908015.1_ASM1690801v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:36,368] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:36,369] [INFO] Found 6/6 markers.
[2024-01-24 11:05:36,401] [INFO] Query marker FASTA was written to GCF_016908015.1_ASM1690801v1_genomic.fna/markers.fasta
[2024-01-24 11:05:36,402] [INFO] Task started: Blastn
[2024-01-24 11:05:36,402] [INFO] Running command: blastn -query GCF_016908015.1_ASM1690801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8365a78a-a8de-42fe-8d02-ab0d189f4cd4/dqc_reference/reference_markers.fasta -out GCF_016908015.1_ASM1690801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:37,015] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:37,018] [INFO] Selected 28 target genomes.
[2024-01-24 11:05:37,019] [INFO] Target genome list was writen to GCF_016908015.1_ASM1690801v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:37,029] [INFO] Task started: fastANI
[2024-01-24 11:05:37,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg499367ec-7485-42e0-93e0-d47c91cb527d/GCF_016908015.1_ASM1690801v1_genomic.fna.gz --refList GCF_016908015.1_ASM1690801v1_genomic.fna/target_genomes.txt --output GCF_016908015.1_ASM1690801v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:57,454] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:57,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8365a78a-a8de-42fe-8d02-ab0d189f4cd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:57,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8365a78a-a8de-42fe-8d02-ab0d189f4cd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:57,497] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:57,498] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:57,498] [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 pascui	strain=DSM 10365	GCA_016908015.1	46609	46609	type	True	100.0	1265	1267	95	conclusive
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	78.2873	337	1267	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	78.1076	352	1267	95	below_threshold
Clostridium liquoris	strain=DSM 100320	GCA_002995785.1	1289519	1289519	type	True	77.8778	254	1267	95	below_threshold
Clostridium rectalis	strain=Marseille-P4200	GCA_900626095.1	2040295	2040295	type	True	77.7591	228	1267	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	77.5959	252	1267	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	77.1885	188	1267	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	77.1063	200	1267	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	77.0417	202	1267	95	below_threshold
Clostridium tetani	strain=ATCC 19406	GCA_000762305.1	1513	1513	type	True	77.0269	209	1267	95	below_threshold
Clostridium tetani	strain=ATCC 19406	GCA_900167265.1	1513	1513	type	True	77.0141	208	1267	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	76.9954	250	1267	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	76.9895	242	1267	95	below_threshold
Clostridium drakei	strain=SL1	GCA_000633595.2	332101	332101	type	True	76.9753	229	1267	95	below_threshold
Clostridium magnum	strain=DSM 2767	GCA_900129955.1	33954	33954	type	True	76.9657	227	1267	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	76.959	209	1267	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_000175595.1	217159	217159	type	True	76.9149	235	1267	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	76.4034	110	1267	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	76.3973	141	1267	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	76.3838	141	1267	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	76.3742	138	1267	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	76.2589	118	1267	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	76.1191	157	1267	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	76.0909	162	1267	95	below_threshold
Inconstantimicrobium porci	strain=WCA-383-APC-5B	GCA_009696465.1	2652291	2652291	type	True	76.045	82	1267	95	below_threshold
Terrisporobacter petrolearius	strain=LAM0A37	GCA_020748185.1	1460447	1460447	type	True	75.2251	76	1267	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:57,500] [INFO] DFAST Taxonomy check result was written to GCF_016908015.1_ASM1690801v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:57,500] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:57,501] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:57,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8365a78a-a8de-42fe-8d02-ab0d189f4cd4/dqc_reference/checkm_data
[2024-01-24 11:05:57,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:57,540] [INFO] Task started: CheckM
[2024-01-24 11:05:57,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908015.1_ASM1690801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908015.1_ASM1690801v1_genomic.fna/checkm_input GCF_016908015.1_ASM1690801v1_genomic.fna/checkm_result
[2024-01-24 11:06:23,911] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:23,913] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:23,936] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:23,937] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:23,937] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908015.1_ASM1690801v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:23,938] [INFO] Task started: Blastn
[2024-01-24 11:06:23,938] [INFO] Running command: blastn -query GCF_016908015.1_ASM1690801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8365a78a-a8de-42fe-8d02-ab0d189f4cd4/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908015.1_ASM1690801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:24,784] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:24,789] [INFO] Selected 19 target genomes.
[2024-01-24 11:06:24,790] [INFO] Target genome list was writen to GCF_016908015.1_ASM1690801v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:24,803] [INFO] Task started: fastANI
[2024-01-24 11:06:24,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg499367ec-7485-42e0-93e0-d47c91cb527d/GCF_016908015.1_ASM1690801v1_genomic.fna.gz --refList GCF_016908015.1_ASM1690801v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908015.1_ASM1690801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:39,087] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:39,101] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:39,101] [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_016908015.1	s__Clostridium_AK pascui	100.0	1265	1267	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	conclusive
GCF_900185645.1	s__Clostridium_AK sp900185645	93.5329	1054	1267	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_900205925.1	s__Clostridium_AK peptidivorans	88.7695	928	1267	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_000619945.1	s__Clostridium_AO lundense	78.2894	337	1267	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_002995785.1	s__Clostridium_AO liquoris	77.864	255	1267	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_900626095.1	s__Clostridium_AS rectalis	77.7587	228	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AS	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009738435.1	s__Clostridium_H bovifaecis	77.6183	182	1267	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_018918285.1	s__MSJ-11 sp018918285	77.6054	253	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__MSJ-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167265.1	s__Clostridium_G tetani	77.0141	208	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_G	95.0	99.11	96.49	0.94	0.90	43	-
GCF_001038625.1	s__Clostridium_AM carboxidivorans	76.986	250	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.96	1.00	0.99	3	-
GCF_000633595.2	s__Clostridium_AM drakei	76.9753	229	1267	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_001889325.1	s__Clostridium_F botulinum_A	76.9339	210	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	95.92	95.51	0.89	0.85	52	-
GCF_000300195.1	s__Clostridium_J tunisiense	76.8569	146	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	96.47	95.03	0.88	0.88	3	-
GCF_000732635.1	s__Clostridium_J sulfidigenes	76.5592	124	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	97.10	95.50	0.86	0.78	28	-
GCF_018861755.1	s__Clostridium_AD sp018861755	76.484	142	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540255.1	s__Clostridium sp900540255	75.8139	107	1267	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_000435835.1	s__Clostridium sp000435835	75.3062	88	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.44	99.22	0.92	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:39,103] [INFO] GTDB search result was written to GCF_016908015.1_ASM1690801v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:39,104] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:39,108] [INFO] DFAST_QC result json was written to GCF_016908015.1_ASM1690801v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:39,108] [INFO] DFAST_QC completed!
[2024-01-24 11:06:39,108] [INFO] Total running time: 0h1m11s