[2024-01-24 15:01:14,933] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:01:14,938] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:01:14,938] [INFO] DQC Reference Directory: /var/lib/cwl/stg88c3af10-bb10-4c05-916e-73fe2f409af7/dqc_reference
[2024-01-24 15:01:16,146] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:01:16,146] [INFO] Task started: Prodigal
[2024-01-24 15:01:16,147] [INFO] Running command: gunzip -c /var/lib/cwl/stga607ed6b-f4e7-4beb-a407-fa49714f6689/GCF_001038625.1_ASM103862v1_genomic.fna.gz | prodigal -d GCF_001038625.1_ASM103862v1_genomic.fna/cds.fna -a GCF_001038625.1_ASM103862v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:01:25,771] [INFO] Task succeeded: Prodigal
[2024-01-24 15:01:25,771] [INFO] Task started: HMMsearch
[2024-01-24 15:01:25,771] [INFO] Running command: hmmsearch --tblout GCF_001038625.1_ASM103862v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88c3af10-bb10-4c05-916e-73fe2f409af7/dqc_reference/reference_markers.hmm GCF_001038625.1_ASM103862v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:01:26,107] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:01:26,108] [INFO] Found 6/6 markers.
[2024-01-24 15:01:26,152] [INFO] Query marker FASTA was written to GCF_001038625.1_ASM103862v1_genomic.fna/markers.fasta
[2024-01-24 15:01:26,152] [INFO] Task started: Blastn
[2024-01-24 15:01:26,153] [INFO] Running command: blastn -query GCF_001038625.1_ASM103862v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88c3af10-bb10-4c05-916e-73fe2f409af7/dqc_reference/reference_markers.fasta -out GCF_001038625.1_ASM103862v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:01:26,734] [INFO] Task succeeded: Blastn
[2024-01-24 15:01:26,741] [INFO] Selected 14 target genomes.
[2024-01-24 15:01:26,741] [INFO] Target genome list was writen to GCF_001038625.1_ASM103862v1_genomic.fna/target_genomes.txt
[2024-01-24 15:01:26,767] [INFO] Task started: fastANI
[2024-01-24 15:01:26,768] [INFO] Running command: fastANI --query /var/lib/cwl/stga607ed6b-f4e7-4beb-a407-fa49714f6689/GCF_001038625.1_ASM103862v1_genomic.fna.gz --refList GCF_001038625.1_ASM103862v1_genomic.fna/target_genomes.txt --output GCF_001038625.1_ASM103862v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:01:43,768] [INFO] Task succeeded: fastANI
[2024-01-24 15:01:43,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88c3af10-bb10-4c05-916e-73fe2f409af7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:01:43,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88c3af10-bb10-4c05-916e-73fe2f409af7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:01:43,785] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:01:43,785] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:01:43,786] [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 carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	100.0	1912	1916	95	conclusive
Clostridium carboxidivorans	strain=P7	GCA_000175595.1	217159	217159	type	True	99.8947	1717	1916	95	conclusive
Clostridium drakei	strain=SL1	GCA_000633595.2	332101	332101	type	True	92.158	1374	1916	95	below_threshold
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	92.1465	1447	1916	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	92.1399	1434	1916	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	87.1022	1228	1916	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	80.0063	497	1916	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	79.7317	691	1916	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	78.0983	274	1916	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	77.8914	273	1916	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	77.5186	159	1916	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.8135	210	1916	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	76.5688	175	1916	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:01:43,788] [INFO] DFAST Taxonomy check result was written to GCF_001038625.1_ASM103862v1_genomic.fna/tc_result.tsv
[2024-01-24 15:01:43,789] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:01:43,789] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:01:43,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88c3af10-bb10-4c05-916e-73fe2f409af7/dqc_reference/checkm_data
[2024-01-24 15:01:43,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:01:43,848] [INFO] Task started: CheckM
[2024-01-24 15:01:43,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001038625.1_ASM103862v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001038625.1_ASM103862v1_genomic.fna/checkm_input GCF_001038625.1_ASM103862v1_genomic.fna/checkm_result
[2024-01-24 15:02:17,479] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:17,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:17,503] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:17,503] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:17,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001038625.1_ASM103862v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:17,504] [INFO] Task started: Blastn
[2024-01-24 15:02:17,504] [INFO] Running command: blastn -query GCF_001038625.1_ASM103862v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88c3af10-bb10-4c05-916e-73fe2f409af7/dqc_reference/reference_markers_gtdb.fasta -out GCF_001038625.1_ASM103862v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:18,292] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:18,295] [INFO] Selected 9 target genomes.
[2024-01-24 15:02:18,295] [INFO] Target genome list was writen to GCF_001038625.1_ASM103862v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:18,306] [INFO] Task started: fastANI
[2024-01-24 15:02:18,306] [INFO] Running command: fastANI --query /var/lib/cwl/stga607ed6b-f4e7-4beb-a407-fa49714f6689/GCF_001038625.1_ASM103862v1_genomic.fna.gz --refList GCF_001038625.1_ASM103862v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001038625.1_ASM103862v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:02:32,058] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:32,067] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:02:32,067] [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_001038625.1	s__Clostridium_AM carboxidivorans	100.0	1912	1916	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	conclusive
GCF_000968375.1	s__Clostridium_AM scatologenes	92.1467	1447	1916	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_000633595.2	s__Clostridium_AM drakei	92.1454	1375	1916	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	87.0884	1230	1916	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_001623875.1	s__Clostridium_AM magnum	79.7087	645	1916	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_001636845.1	s__Clostridium_B ljungdahlii_A	79.7009	490	1916	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_019207025.1	s__Clostridium_AM sp019207025	79.6933	697	1916	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	78.9097	545	1916	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_016908015.1	s__Clostridium_AK pascui	76.8979	256	1916	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	-
--------------------------------------------------------------------------------
[2024-01-24 15:02:32,069] [INFO] GTDB search result was written to GCF_001038625.1_ASM103862v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:02:32,069] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:02:32,073] [INFO] DFAST_QC result json was written to GCF_001038625.1_ASM103862v1_genomic.fna/dqc_result.json
[2024-01-24 15:02:32,074] [INFO] DFAST_QC completed!
[2024-01-24 15:02:32,074] [INFO] Total running time: 0h1m17s