[2024-01-24 13:21:47,243] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:47,247] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:47,247] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f411314-eb8f-4fa9-8ff1-09ddb159eb6c/dqc_reference
[2024-01-24 13:21:48,576] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:48,577] [INFO] Task started: Prodigal
[2024-01-24 13:21:48,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg88ed8bad-1935-43c7-9f69-9488c9c02f83/GCF_019207025.1_ASM1920702v1_genomic.fna.gz | prodigal -d GCF_019207025.1_ASM1920702v1_genomic.fna/cds.fna -a GCF_019207025.1_ASM1920702v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:58,593] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:58,594] [INFO] Task started: HMMsearch
[2024-01-24 13:21:58,594] [INFO] Running command: hmmsearch --tblout GCF_019207025.1_ASM1920702v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f411314-eb8f-4fa9-8ff1-09ddb159eb6c/dqc_reference/reference_markers.hmm GCF_019207025.1_ASM1920702v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:58,970] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:58,971] [INFO] Found 6/6 markers.
[2024-01-24 13:21:59,024] [INFO] Query marker FASTA was written to GCF_019207025.1_ASM1920702v1_genomic.fna/markers.fasta
[2024-01-24 13:21:59,025] [INFO] Task started: Blastn
[2024-01-24 13:21:59,025] [INFO] Running command: blastn -query GCF_019207025.1_ASM1920702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f411314-eb8f-4fa9-8ff1-09ddb159eb6c/dqc_reference/reference_markers.fasta -out GCF_019207025.1_ASM1920702v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:59,661] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:59,670] [INFO] Selected 15 target genomes.
[2024-01-24 13:21:59,671] [INFO] Target genome list was writen to GCF_019207025.1_ASM1920702v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:59,679] [INFO] Task started: fastANI
[2024-01-24 13:21:59,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg88ed8bad-1935-43c7-9f69-9488c9c02f83/GCF_019207025.1_ASM1920702v1_genomic.fna.gz --refList GCF_019207025.1_ASM1920702v1_genomic.fna/target_genomes.txt --output GCF_019207025.1_ASM1920702v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:15,879] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:15,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f411314-eb8f-4fa9-8ff1-09ddb159eb6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:15,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f411314-eb8f-4fa9-8ff1-09ddb159eb6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:15,894] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:15,894] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:15,895] [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 thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	100.0	2024	2033	95	conclusive
Clostridium aciditolerans	strain=DSM 17425	GCA_016316925.1	339861	339861	type	True	80.8829	765	2033	95	below_threshold
Clostridium magnum	strain=DSM 2767	GCA_900129955.1	33954	33954	type	True	80.2137	706	2033	95	below_threshold
Clostridium drakei	strain=SL1	GCA_000633595.2	332101	332101	type	True	79.5831	686	2033	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	79.562	700	2033	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_000175595.1	217159	217159	type	True	79.5127	669	2033	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	79.476	709	2033	95	below_threshold
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	79.464	703	2033	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	79.2481	605	2033	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	77.8528	369	2033	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	77.3056	219	2033	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	77.2809	221	2033	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.3947	152	2033	95	below_threshold
Oceanirhabdus seepicola	strain=ZWT	GCA_023684385.1	2828781	2828781	type	True	75.7242	126	2033	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:15,897] [INFO] DFAST Taxonomy check result was written to GCF_019207025.1_ASM1920702v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:15,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:15,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:15,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f411314-eb8f-4fa9-8ff1-09ddb159eb6c/dqc_reference/checkm_data
[2024-01-24 13:22:15,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:15,978] [INFO] Task started: CheckM
[2024-01-24 13:22:15,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019207025.1_ASM1920702v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019207025.1_ASM1920702v1_genomic.fna/checkm_input GCF_019207025.1_ASM1920702v1_genomic.fna/checkm_result
[2024-01-24 13:22:52,617] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:52,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:52,636] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:52,636] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:52,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019207025.1_ASM1920702v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:52,637] [INFO] Task started: Blastn
[2024-01-24 13:22:52,637] [INFO] Running command: blastn -query GCF_019207025.1_ASM1920702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f411314-eb8f-4fa9-8ff1-09ddb159eb6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_019207025.1_ASM1920702v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:53,474] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:53,477] [INFO] Selected 16 target genomes.
[2024-01-24 13:22:53,477] [INFO] Target genome list was writen to GCF_019207025.1_ASM1920702v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:53,489] [INFO] Task started: fastANI
[2024-01-24 13:22:53,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg88ed8bad-1935-43c7-9f69-9488c9c02f83/GCF_019207025.1_ASM1920702v1_genomic.fna.gz --refList GCF_019207025.1_ASM1920702v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019207025.1_ASM1920702v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:09,746] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:09,759] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:09,760] [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_019207025.1	s__Clostridium_AM sp019207025	100.0	2024	2033	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	conclusive
GCF_016316925.1	s__Clostridium_AM aciditolerans	80.918	759	2033	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_001623875.1	s__Clostridium_AM magnum	80.2233	707	2033	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	-
GCF_000633595.2	s__Clostridium_AM drakei	79.5716	688	2033	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_001038625.1	s__Clostridium_AM carboxidivorans	79.4829	707	2033	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	79.4575	707	2033	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_012926525.1	s__Clostridium_AM sp012926525	79.2728	601	2033	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_014050525.1	s__Clostridium_B sp014050525	76.9664	172	2033	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_016765585.1	s__F0540 sp016765585	76.667	180	2033	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861705.1	s__Clostridium_AD psychrophilum	76.0198	153	2033	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_015058475.1	s__Clostridium butyricum_B	75.7854	129	2033	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 13:23:09,761] [INFO] GTDB search result was written to GCF_019207025.1_ASM1920702v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:09,762] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:09,766] [INFO] DFAST_QC result json was written to GCF_019207025.1_ASM1920702v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:09,766] [INFO] DFAST_QC completed!
[2024-01-24 13:23:09,766] [INFO] Total running time: 0h1m23s