[2024-01-24 13:40:33,366] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:33,368] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:33,368] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8002e57-4cb3-41fe-b181-8d6e22cd4e13/dqc_reference
[2024-01-24 13:40:34,646] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:34,647] [INFO] Task started: Prodigal
[2024-01-24 13:40:34,647] [INFO] Running command: gunzip -c /var/lib/cwl/stg93b028d7-17c9-4663-ae6d-b67fa5d5ff27/GCF_001623875.1_ASM162387v1_genomic.fna.gz | prodigal -d GCF_001623875.1_ASM162387v1_genomic.fna/cds.fna -a GCF_001623875.1_ASM162387v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:45,751] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:45,751] [INFO] Task started: HMMsearch
[2024-01-24 13:40:45,751] [INFO] Running command: hmmsearch --tblout GCF_001623875.1_ASM162387v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8002e57-4cb3-41fe-b181-8d6e22cd4e13/dqc_reference/reference_markers.hmm GCF_001623875.1_ASM162387v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:46,160] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:46,162] [INFO] Found 6/6 markers.
[2024-01-24 13:40:46,212] [INFO] Query marker FASTA was written to GCF_001623875.1_ASM162387v1_genomic.fna/markers.fasta
[2024-01-24 13:40:46,213] [INFO] Task started: Blastn
[2024-01-24 13:40:46,213] [INFO] Running command: blastn -query GCF_001623875.1_ASM162387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8002e57-4cb3-41fe-b181-8d6e22cd4e13/dqc_reference/reference_markers.fasta -out GCF_001623875.1_ASM162387v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:46,844] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:46,847] [INFO] Selected 26 target genomes.
[2024-01-24 13:40:46,848] [INFO] Target genome list was writen to GCF_001623875.1_ASM162387v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:46,872] [INFO] Task started: fastANI
[2024-01-24 13:40:46,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg93b028d7-17c9-4663-ae6d-b67fa5d5ff27/GCF_001623875.1_ASM162387v1_genomic.fna.gz --refList GCF_001623875.1_ASM162387v1_genomic.fna/target_genomes.txt --output GCF_001623875.1_ASM162387v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:13,224] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:13,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8002e57-4cb3-41fe-b181-8d6e22cd4e13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:13,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8002e57-4cb3-41fe-b181-8d6e22cd4e13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:13,248] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:13,248] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:13,249] [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 magnum	strain=DSM 2767	GCA_001623875.1	33954	33954	type	True	100.0	2198	2200	95	conclusive
Clostridium magnum	strain=DSM 2767	GCA_900129955.1	33954	33954	type	True	99.9316	2070	2200	95	conclusive
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	80.1722	705	2200	95	below_threshold
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	79.7819	658	2200	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	79.7023	627	2200	95	below_threshold
Clostridium aciditolerans	strain=DSM 17425	GCA_016316925.1	339861	339861	type	True	79.4855	584	2200	95	below_threshold
Clostridium drakei	strain=SL1	GCA_000633595.2	332101	332101	type	True	79.4015	601	2200	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	79.187	563	2200	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	79.0249	361	2200	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	77.9331	245	2200	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	77.8295	246	2200	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	77.6744	189	2200	95	below_threshold
Clostridium hydrogenum	strain=CUEA01	GCA_021432385.1	2855764	2855764	type	True	77.6576	218	2200	95	below_threshold
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	77.1332	194	2200	95	below_threshold
Clostridium pascui	strain=DSM 10365	GCA_016908015.1	46609	46609	type	True	77.0857	234	2200	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	76.9057	225	2200	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	76.2169	145	2200	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	76.0398	132	2200	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	75.8653	148	2200	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:13,250] [INFO] DFAST Taxonomy check result was written to GCF_001623875.1_ASM162387v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:13,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:13,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:13,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8002e57-4cb3-41fe-b181-8d6e22cd4e13/dqc_reference/checkm_data
[2024-01-24 13:41:13,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:13,329] [INFO] Task started: CheckM
[2024-01-24 13:41:13,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001623875.1_ASM162387v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001623875.1_ASM162387v1_genomic.fna/checkm_input GCF_001623875.1_ASM162387v1_genomic.fna/checkm_result
[2024-01-24 13:41:52,418] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:52,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:52,450] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:52,450] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:52,451] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001623875.1_ASM162387v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:52,451] [INFO] Task started: Blastn
[2024-01-24 13:41:52,451] [INFO] Running command: blastn -query GCF_001623875.1_ASM162387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8002e57-4cb3-41fe-b181-8d6e22cd4e13/dqc_reference/reference_markers_gtdb.fasta -out GCF_001623875.1_ASM162387v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:53,271] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:53,276] [INFO] Selected 22 target genomes.
[2024-01-24 13:41:53,277] [INFO] Target genome list was writen to GCF_001623875.1_ASM162387v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:53,302] [INFO] Task started: fastANI
[2024-01-24 13:41:53,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg93b028d7-17c9-4663-ae6d-b67fa5d5ff27/GCF_001623875.1_ASM162387v1_genomic.fna.gz --refList GCF_001623875.1_ASM162387v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001623875.1_ASM162387v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:12,811] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:12,824] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:12,825] [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_001623875.1	s__Clostridium_AM magnum	100.0	2198	2200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCF_019207025.1	s__Clostridium_AM sp019207025	80.2014	701	2200	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_001038625.1	s__Clostridium_AM carboxidivorans	80.1847	655	2200	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_000968375.1	s__Clostridium_AM scatologenes	79.8019	658	2200	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_016316925.1	s__Clostridium_AM aciditolerans	79.455	588	2200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	95.27	95.27	0.80	0.80	2	-
GCF_000633595.2	s__Clostridium_AM drakei	79.4066	601	2200	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_012926525.1	s__Clostridium_AM sp012926525	79.1414	569	2200	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_003718715.1	s__JN-1 sp003718715	78.4595	265	2200	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_001675165.1	s__Clostridium_B ragsdalei	78.3565	338	2200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	98.18	98.18	0.88	0.88	2	-
GCF_000014125.1	s__Clostridium_H novyi	77.4884	174	2200	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_900185645.1	s__Clostridium_AK sp900185645	77.422	231	2200	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_001243045.1	s__Clostridium_F niameyense	77.1272	194	2200	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_002008345.1	s__Clostridium_F tepidum	76.9162	224	2200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
GCA_002341865.1	s__Clostridium_J sp002341865	76.276	192	2200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836325.1	s__Clostridium sp014836325	76.2115	143	2200	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_002400085.1	s__UBA4839 sp002400085	75.4725	69	2200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__UBA4839	95.0	99.41	99.11	0.85	0.82	15	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:12,826] [INFO] GTDB search result was written to GCF_001623875.1_ASM162387v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:12,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:12,833] [INFO] DFAST_QC result json was written to GCF_001623875.1_ASM162387v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:12,833] [INFO] DFAST_QC completed!
[2024-01-24 13:42:12,833] [INFO] Total running time: 0h1m39s