[2024-01-24 14:05:47,113] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:47,115] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:47,115] [INFO] DQC Reference Directory: /var/lib/cwl/stg55d89320-f957-428f-b122-af44edab3bb6/dqc_reference
[2024-01-24 14:05:48,412] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:48,413] [INFO] Task started: Prodigal
[2024-01-24 14:05:48,413] [INFO] Running command: gunzip -c /var/lib/cwl/stge72b40ef-5fcc-41b5-b45b-a979ca47f511/GCF_009695815.1_ASM969581v1_genomic.fna.gz | prodigal -d GCF_009695815.1_ASM969581v1_genomic.fna/cds.fna -a GCF_009695815.1_ASM969581v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:53,209] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:53,209] [INFO] Task started: HMMsearch
[2024-01-24 14:05:53,210] [INFO] Running command: hmmsearch --tblout GCF_009695815.1_ASM969581v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55d89320-f957-428f-b122-af44edab3bb6/dqc_reference/reference_markers.hmm GCF_009695815.1_ASM969581v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:53,457] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:53,458] [INFO] Found 6/6 markers.
[2024-01-24 14:05:53,494] [INFO] Query marker FASTA was written to GCF_009695815.1_ASM969581v1_genomic.fna/markers.fasta
[2024-01-24 14:05:53,495] [INFO] Task started: Blastn
[2024-01-24 14:05:53,495] [INFO] Running command: blastn -query GCF_009695815.1_ASM969581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55d89320-f957-428f-b122-af44edab3bb6/dqc_reference/reference_markers.fasta -out GCF_009695815.1_ASM969581v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:54,100] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:54,105] [INFO] Selected 22 target genomes.
[2024-01-24 14:05:54,105] [INFO] Target genome list was writen to GCF_009695815.1_ASM969581v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:54,115] [INFO] Task started: fastANI
[2024-01-24 14:05:54,115] [INFO] Running command: fastANI --query /var/lib/cwl/stge72b40ef-5fcc-41b5-b45b-a979ca47f511/GCF_009695815.1_ASM969581v1_genomic.fna.gz --refList GCF_009695815.1_ASM969581v1_genomic.fna/target_genomes.txt --output GCF_009695815.1_ASM969581v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:06,320] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:06,321] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55d89320-f957-428f-b122-af44edab3bb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:06,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55d89320-f957-428f-b122-af44edab3bb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:06,340] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:06,340] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:06,341] [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
Peptostreptococcus porci	strain=WCA-SAB-591-4A-A	GCA_009695815.1	2652282	2652282	type	True	100.0	715	716	95	conclusive
Peptostreptococcus stomatis	strain=DSM 17678	GCA_000147675.2	341694	341694	type	True	79.4576	83	716	95	below_threshold
Peptostreptococcus anaerobius	strain=NCTC11460	GCA_900454605.1	1261	1261	type	True	79.1891	112	716	95	below_threshold
Peptostreptococcus anaerobius	strain=DSM 2949	GCA_000381525.1	1261	1261	type	True	78.8548	106	716	95	below_threshold
Peptostreptococcus anaerobius	strain=VPI 4330	GCA_000318115.1	1261	1261	type	True	78.5816	104	716	95	below_threshold
Peptostreptococcus canis	strain=DSM 27025	GCA_014229965.1	1159213	1159213	type	True	78.4742	163	716	95	below_threshold
Peptostreptococcus canis	strain=DSM 27025	GCA_017874285.1	1159213	1159213	type	True	78.4364	162	716	95	below_threshold
Peptostreptococcus russellii	strain=RT-10B	GCA_003012055.1	215200	215200	type	True	78.3071	132	716	95	below_threshold
Terrisporobacter mayombei	strain=DSM 6539	GCA_020748465.1	1541	1541	type	True	76.325	58	716	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	76.1354	63	716	95	below_threshold
Paraclostridium bifermentans subsp. muricolitidis	strain=PAGU 1678	GCA_019650315.1	2663173	1490	type	True	76.0071	54	716	95	below_threshold
Terrisporobacter othiniensis	strain=08-306576	GCA_000808015.1	1577792	1577792	type	True	75.9849	57	716	95	below_threshold
Terrisporobacter glycolicus	strain=ATCC 14880	GCA_000373865.1	36841	36841	suspected-type	True	75.9667	60	716	95	below_threshold
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	75.6892	58	716	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	75.6508	59	716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:06,343] [INFO] DFAST Taxonomy check result was written to GCF_009695815.1_ASM969581v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:06,344] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:06,344] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:06,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55d89320-f957-428f-b122-af44edab3bb6/dqc_reference/checkm_data
[2024-01-24 14:06:06,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:06,372] [INFO] Task started: CheckM
[2024-01-24 14:06:06,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009695815.1_ASM969581v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009695815.1_ASM969581v1_genomic.fna/checkm_input GCF_009695815.1_ASM969581v1_genomic.fna/checkm_result
[2024-01-24 14:06:28,327] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:28,328] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:28,349] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:28,349] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:28,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009695815.1_ASM969581v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:28,350] [INFO] Task started: Blastn
[2024-01-24 14:06:28,350] [INFO] Running command: blastn -query GCF_009695815.1_ASM969581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55d89320-f957-428f-b122-af44edab3bb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_009695815.1_ASM969581v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:29,156] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:29,160] [INFO] Selected 19 target genomes.
[2024-01-24 14:06:29,160] [INFO] Target genome list was writen to GCF_009695815.1_ASM969581v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:29,180] [INFO] Task started: fastANI
[2024-01-24 14:06:29,182] [INFO] Running command: fastANI --query /var/lib/cwl/stge72b40ef-5fcc-41b5-b45b-a979ca47f511/GCF_009695815.1_ASM969581v1_genomic.fna.gz --refList GCF_009695815.1_ASM969581v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009695815.1_ASM969581v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:38,535] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:38,548] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:38,548] [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_009695815.1	s__Peptostreptococcus porci	100.0	715	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112955.1	s__Peptostreptococcus sp900112955	91.7581	572	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000147675.1	s__Peptostreptococcus stomatis	79.4576	83	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCF_000758885.1	s__Peptostreptococcus sp000758885	78.9981	79	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381525.1	s__Peptostreptococcus anaerobius	78.8321	106	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	99.16	98.74	0.90	0.83	12	-
GCA_900759325.1	s__Peptostreptococcus sp900759325	78.5378	87	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	98.17	97.99	0.91	0.90	4	-
GCF_014229965.1	s__Peptostreptococcus canis	78.4502	164	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003012055.1	s__Peptostreptococcus russellii	78.3071	132	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	98.54	98.54	0.93	0.93	2	-
GCF_900110295.1	s__Peptostreptococcus russellii_A	78.0275	130	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	98.51	98.15	0.92	0.90	3	-
GCF_015668515.1	s__Paraclostridium tenue	76.3753	54	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.58	97.73	0.92	0.87	8	-
GCF_000449425.2	s__Clostridioides difficile_E	76.375	66	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006802875.1	s__Paraclostridium bifermentans	75.6508	59	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.64	96.79	0.90	0.86	14	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:38,552] [INFO] GTDB search result was written to GCF_009695815.1_ASM969581v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:38,553] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:38,558] [INFO] DFAST_QC result json was written to GCF_009695815.1_ASM969581v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:38,558] [INFO] DFAST_QC completed!
[2024-01-24 14:06:38,558] [INFO] Total running time: 0h0m51s