[2023-06-14 02:11:11,609] [INFO] DFAST_QC pipeline started.
[2023-06-14 02:11:11,615] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 02:11:11,615] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5a20159-3df1-4c6d-9fd8-b9d3496de4a2/dqc_reference
[2023-06-14 02:11:13,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 02:11:13,416] [INFO] Task started: Prodigal
[2023-06-14 02:11:13,416] [INFO] Running command: gunzip -c /var/lib/cwl/stg87bdcc6c-805e-416b-b916-4f45b54ba920/GCA_022646985.1_ASM2264698v1_genomic.fna.gz | prodigal -d GCA_022646985.1_ASM2264698v1_genomic.fna/cds.fna -a GCA_022646985.1_ASM2264698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 02:11:22,037] [INFO] Task succeeded: Prodigal
[2023-06-14 02:11:22,037] [INFO] Task started: HMMsearch
[2023-06-14 02:11:22,037] [INFO] Running command: hmmsearch --tblout GCA_022646985.1_ASM2264698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5a20159-3df1-4c6d-9fd8-b9d3496de4a2/dqc_reference/reference_markers.hmm GCA_022646985.1_ASM2264698v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 02:11:22,408] [INFO] Task succeeded: HMMsearch
[2023-06-14 02:11:22,409] [INFO] Found 6/6 markers.
[2023-06-14 02:11:22,452] [INFO] Query marker FASTA was written to GCA_022646985.1_ASM2264698v1_genomic.fna/markers.fasta
[2023-06-14 02:11:22,452] [INFO] Task started: Blastn
[2023-06-14 02:11:22,452] [INFO] Running command: blastn -query GCA_022646985.1_ASM2264698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5a20159-3df1-4c6d-9fd8-b9d3496de4a2/dqc_reference/reference_markers.fasta -out GCA_022646985.1_ASM2264698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 02:11:23,093] [INFO] Task succeeded: Blastn
[2023-06-14 02:11:23,097] [INFO] Selected 11 target genomes.
[2023-06-14 02:11:23,097] [INFO] Target genome list was writen to GCA_022646985.1_ASM2264698v1_genomic.fna/target_genomes.txt
[2023-06-14 02:11:23,103] [INFO] Task started: fastANI
[2023-06-14 02:11:23,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg87bdcc6c-805e-416b-b916-4f45b54ba920/GCA_022646985.1_ASM2264698v1_genomic.fna.gz --refList GCA_022646985.1_ASM2264698v1_genomic.fna/target_genomes.txt --output GCA_022646985.1_ASM2264698v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 02:11:40,436] [INFO] Task succeeded: fastANI
[2023-06-14 02:11:40,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5a20159-3df1-4c6d-9fd8-b9d3496de4a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 02:11:40,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5a20159-3df1-4c6d-9fd8-b9d3496de4a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 02:11:40,446] [INFO] Found 8 fastANI hits (5 hits with ANI > threshold)
[2023-06-14 02:11:40,447] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-14 02:11:40,447] [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 beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	98.0311	1487	1777	95	inconclusive
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	98.0003	1569	1777	95	inconclusive
Clostridium beijerinckii	strain=NCTC13035	GCA_900447025.1	1520	1520	suspected-type	True	97.9958	1576	1777	95	inconclusive
Clostridium diolis	strain=DSM 15410	GCA_008705175.1	223919	223919	suspected-type	True	97.875	1590	1777	95	inconclusive
Clostridium diolis	strain=DSM 15410	GCA_008580445.1	223919	223919	suspected-type	True	97.8528	1590	1777	95	inconclusive
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	81.0847	885	1777	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	78.4733	383	1777	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	78.4533	449	1777	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 02:11:40,468] [INFO] DFAST Taxonomy check result was written to GCA_022646985.1_ASM2264698v1_genomic.fna/tc_result.tsv
[2023-06-14 02:11:40,470] [INFO] ===== Taxonomy check completed =====
[2023-06-14 02:11:40,470] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 02:11:40,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5a20159-3df1-4c6d-9fd8-b9d3496de4a2/dqc_reference/checkm_data
[2023-06-14 02:11:40,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 02:11:40,538] [INFO] Task started: CheckM
[2023-06-14 02:11:40,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022646985.1_ASM2264698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022646985.1_ASM2264698v1_genomic.fna/checkm_input GCA_022646985.1_ASM2264698v1_genomic.fna/checkm_result
[2023-06-14 02:12:11,193] [INFO] Task succeeded: CheckM
[2023-06-14 02:12:11,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 02:12:11,218] [INFO] ===== Completeness check finished =====
[2023-06-14 02:12:11,218] [INFO] ===== Start GTDB Search =====
[2023-06-14 02:12:11,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022646985.1_ASM2264698v1_genomic.fna/markers.fasta)
[2023-06-14 02:12:11,219] [INFO] Task started: Blastn
[2023-06-14 02:12:11,219] [INFO] Running command: blastn -query GCA_022646985.1_ASM2264698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5a20159-3df1-4c6d-9fd8-b9d3496de4a2/dqc_reference/reference_markers_gtdb.fasta -out GCA_022646985.1_ASM2264698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 02:12:11,965] [INFO] Task succeeded: Blastn
[2023-06-14 02:12:11,971] [INFO] Selected 13 target genomes.
[2023-06-14 02:12:11,971] [INFO] Target genome list was writen to GCA_022646985.1_ASM2264698v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 02:12:11,982] [INFO] Task started: fastANI
[2023-06-14 02:12:11,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg87bdcc6c-805e-416b-b916-4f45b54ba920/GCA_022646985.1_ASM2264698v1_genomic.fna.gz --refList GCA_022646985.1_ASM2264698v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022646985.1_ASM2264698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 02:12:28,549] [INFO] Task succeeded: fastANI
[2023-06-14 02:12:28,569] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 02:12:28,569] [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_018223745.1	s__Clostridium beijerinckii	97.9939	1569	1777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.01	95.18	0.85	0.79	244	conclusive
GCF_000621745.1	s__Clostridium beijerinckii_A	92.418	1475	1777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002029255.1	s__Clostridium chromiireducens	82.8141	981	1777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.07	97.40	0.90	0.87	3	-
GCF_002760435.1	s__Clostridium sp002760435	81.8406	939	1777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000230835.1	s__Clostridium sp000230835	81.7936	969	1777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.12	96.12	0.82	0.82	2	-
GCA_003129525.1	s__Clostridium beijerinckii_D	81.4849	811	1777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002006345.1	s__Clostridium puniceum	80.8961	819	1777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340885.1	s__Clostridium saccharoperbutylacetonicum	80.8329	899	1777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.35	98.00	0.96	0.89	7	-
GCF_009928485.1	s__Clostridium sp009928485	80.6072	818	1777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473995.1	s__Clostridium saccharobutylicum	80.3849	707	1777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.89	95.82	0.99	0.83	65	-
GCA_900769625.1	s__Clostridium sp900769625	78.5384	330	1777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290265.1	s__Clostridium cagae	78.4533	384	1777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.09	97.56	0.90	0.85	15	-
GCF_001735765.2	s__Clostridium taeniosporum	78.1308	396	1777	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 02:12:28,571] [INFO] GTDB search result was written to GCA_022646985.1_ASM2264698v1_genomic.fna/result_gtdb.tsv
[2023-06-14 02:12:28,572] [INFO] ===== GTDB Search completed =====
[2023-06-14 02:12:28,575] [INFO] DFAST_QC result json was written to GCA_022646985.1_ASM2264698v1_genomic.fna/dqc_result.json
[2023-06-14 02:12:28,575] [INFO] DFAST_QC completed!
[2023-06-14 02:12:28,576] [INFO] Total running time: 0h1m17s