[2024-01-24 13:10:19,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:19,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:19,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bdc226c-e035-401c-9740-59b90604b192/dqc_reference
[2024-01-24 13:10:20,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:20,769] [INFO] Task started: Prodigal
[2024-01-24 13:10:20,770] [INFO] Running command: gunzip -c /var/lib/cwl/stgc44b7b49-9700-4d08-8fb2-c4a7b365fa97/GCF_003096175.1_ASM309617v1_genomic.fna.gz | prodigal -d GCF_003096175.1_ASM309617v1_genomic.fna/cds.fna -a GCF_003096175.1_ASM309617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:30,379] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:30,379] [INFO] Task started: HMMsearch
[2024-01-24 13:10:30,379] [INFO] Running command: hmmsearch --tblout GCF_003096175.1_ASM309617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bdc226c-e035-401c-9740-59b90604b192/dqc_reference/reference_markers.hmm GCF_003096175.1_ASM309617v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:30,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:30,758] [INFO] Found 6/6 markers.
[2024-01-24 13:10:30,804] [INFO] Query marker FASTA was written to GCF_003096175.1_ASM309617v1_genomic.fna/markers.fasta
[2024-01-24 13:10:30,805] [INFO] Task started: Blastn
[2024-01-24 13:10:30,805] [INFO] Running command: blastn -query GCF_003096175.1_ASM309617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bdc226c-e035-401c-9740-59b90604b192/dqc_reference/reference_markers.fasta -out GCF_003096175.1_ASM309617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:31,483] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:31,489] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:31,489] [INFO] Target genome list was writen to GCF_003096175.1_ASM309617v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:31,494] [INFO] Task started: fastANI
[2024-01-24 13:10:31,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgc44b7b49-9700-4d08-8fb2-c4a7b365fa97/GCF_003096175.1_ASM309617v1_genomic.fna.gz --refList GCF_003096175.1_ASM309617v1_genomic.fna/target_genomes.txt --output GCF_003096175.1_ASM309617v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:48,128] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:48,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bdc226c-e035-401c-9740-59b90604b192/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:48,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bdc226c-e035-401c-9740-59b90604b192/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:48,143] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:10:48,143] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:10:48,144] [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 drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	100.0	1896	1898	95	inconclusive
Clostridium drakei	strain=SL1	GCA_000633595.2	332101	332101	type	True	99.9576	1797	1898	95	inconclusive
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	96.0468	1634	1898	95	inconclusive
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	92.2058	1426	1898	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_000175595.1	217159	217159	type	True	92.0715	1315	1898	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	86.358	1177	1898	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	79.7093	508	1898	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	79.5635	714	1898	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	77.5574	290	1898	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	77.5041	286	1898	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	76.9062	235	1898	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.4733	200	1898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:48,148] [INFO] DFAST Taxonomy check result was written to GCF_003096175.1_ASM309617v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:48,155] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:48,155] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:48,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bdc226c-e035-401c-9740-59b90604b192/dqc_reference/checkm_data
[2024-01-24 13:10:48,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:48,216] [INFO] Task started: CheckM
[2024-01-24 13:10:48,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003096175.1_ASM309617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003096175.1_ASM309617v1_genomic.fna/checkm_input GCF_003096175.1_ASM309617v1_genomic.fna/checkm_result
[2024-01-24 13:11:22,385] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:22,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:22,408] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:22,409] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:22,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003096175.1_ASM309617v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:22,409] [INFO] Task started: Blastn
[2024-01-24 13:11:22,410] [INFO] Running command: blastn -query GCF_003096175.1_ASM309617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bdc226c-e035-401c-9740-59b90604b192/dqc_reference/reference_markers_gtdb.fasta -out GCF_003096175.1_ASM309617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:23,169] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:23,175] [INFO] Selected 9 target genomes.
[2024-01-24 13:11:23,175] [INFO] Target genome list was writen to GCF_003096175.1_ASM309617v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:23,180] [INFO] Task started: fastANI
[2024-01-24 13:11:23,181] [INFO] Running command: fastANI --query /var/lib/cwl/stgc44b7b49-9700-4d08-8fb2-c4a7b365fa97/GCF_003096175.1_ASM309617v1_genomic.fna.gz --refList GCF_003096175.1_ASM309617v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003096175.1_ASM309617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:36,465] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:36,480] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:36,481] [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_000633595.2	s__Clostridium_AM drakei	99.9576	1797	1898	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	conclusive
GCF_000968375.1	s__Clostridium_AM scatologenes	96.0568	1634	1898	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_001038625.1	s__Clostridium_AM carboxidivorans	92.2072	1426	1898	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_012926525.1	s__Clostridium_AM sp012926525	86.3555	1176	1898	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_000143685.1	s__Clostridium_B ljungdahlii	79.9327	530	1898	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	98.76	97.79	0.92	0.88	9	-
GCF_001623875.1	s__Clostridium_AM magnum	79.637	611	1898	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_019207025.1	s__Clostridium_AM sp019207025	79.5686	714	1898	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_016316925.1	s__Clostridium_AM aciditolerans	78.8459	521	1898	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_900185645.1	s__Clostridium_AK sp900185645	77.4212	234	1898	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:36,483] [INFO] GTDB search result was written to GCF_003096175.1_ASM309617v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:36,483] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:36,487] [INFO] DFAST_QC result json was written to GCF_003096175.1_ASM309617v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:36,487] [INFO] DFAST_QC completed!
[2024-01-24 13:11:36,487] [INFO] Total running time: 0h1m17s