[2024-01-24 13:46:29,599] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:29,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:29,601] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa27abc5-8789-4eb8-918f-bf0c2bde3105/dqc_reference
[2024-01-24 13:46:30,874] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:30,875] [INFO] Task started: Prodigal
[2024-01-24 13:46:30,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a8564f3-463e-4d3e-833d-59c0e4f041e1/GCF_012849095.1_ASM1284909v1_genomic.fna.gz | prodigal -d GCF_012849095.1_ASM1284909v1_genomic.fna/cds.fna -a GCF_012849095.1_ASM1284909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:53,922] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:53,923] [INFO] Task started: HMMsearch
[2024-01-24 13:46:53,923] [INFO] Running command: hmmsearch --tblout GCF_012849095.1_ASM1284909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa27abc5-8789-4eb8-918f-bf0c2bde3105/dqc_reference/reference_markers.hmm GCF_012849095.1_ASM1284909v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:54,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:54,357] [INFO] Found 6/6 markers.
[2024-01-24 13:46:54,429] [INFO] Query marker FASTA was written to GCF_012849095.1_ASM1284909v1_genomic.fna/markers.fasta
[2024-01-24 13:46:54,430] [INFO] Task started: Blastn
[2024-01-24 13:46:54,430] [INFO] Running command: blastn -query GCF_012849095.1_ASM1284909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa27abc5-8789-4eb8-918f-bf0c2bde3105/dqc_reference/reference_markers.fasta -out GCF_012849095.1_ASM1284909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:55,030] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:55,034] [INFO] Selected 16 target genomes.
[2024-01-24 13:46:55,035] [INFO] Target genome list was writen to GCF_012849095.1_ASM1284909v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:55,048] [INFO] Task started: fastANI
[2024-01-24 13:46:55,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a8564f3-463e-4d3e-833d-59c0e4f041e1/GCF_012849095.1_ASM1284909v1_genomic.fna.gz --refList GCF_012849095.1_ASM1284909v1_genomic.fna/target_genomes.txt --output GCF_012849095.1_ASM1284909v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:12,830] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:12,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa27abc5-8789-4eb8-918f-bf0c2bde3105/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:12,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa27abc5-8789-4eb8-918f-bf0c2bde3105/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:12,843] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:12,843] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:12,844] [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
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	100.0	2839	2840	95	conclusive
Cohnella cholangitidis	strain=1605-214	GCA_014107495.1	2598458	2598458	type	True	81.318	1068	2840	95	below_threshold
Cohnella luojiensis	strain=CCTCC AB 208254	GCA_004564235.1	652876	652876	type	True	80.0785	658	2840	95	below_threshold
Cohnella endophytica	strain=M2MS4P-1	GCA_003628305.1	2419778	2419778	type	True	79.9985	720	2840	95	below_threshold
Cohnella lupini	strain=CECT 8236	GCA_003386205.1	1294267	1294267	type	True	79.9053	735	2840	95	below_threshold
Cohnella abietis	strain=HS21	GCA_004295585.1	2507935	2507935	type	True	79.4354	520	2840	95	below_threshold
Cohnella terricola	strain=G13	GCA_007786475.1	1289167	1289167	type	True	79.1218	601	2840	95	below_threshold
Cohnella panacarvi	strain=Gsoil 349	GCA_000515335.1	400776	400776	type	True	78.0501	359	2840	95	below_threshold
Cohnella kolymensis	strain=VKM B-2846	GCA_000829465.1	1590652	1590652	type	True	77.9514	251	2840	95	below_threshold
Cohnella faecalis	strain=K2E09-144	GCA_003570905.1	2315694	2315694	type	True	77.9478	328	2840	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	77.8531	53	2840	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	77.5796	58	2840	95	below_threshold
Paenibacillus anseongense	strain=MAH-34	GCA_009757995.1	2682845	2682845	type	True	76.5812	84	2840	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.4138	102	2840	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	76.253	113	2840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:12,845] [INFO] DFAST Taxonomy check result was written to GCF_012849095.1_ASM1284909v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:12,846] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:12,846] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:12,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa27abc5-8789-4eb8-918f-bf0c2bde3105/dqc_reference/checkm_data
[2024-01-24 13:47:12,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:12,925] [INFO] Task started: CheckM
[2024-01-24 13:47:12,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012849095.1_ASM1284909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012849095.1_ASM1284909v1_genomic.fna/checkm_input GCF_012849095.1_ASM1284909v1_genomic.fna/checkm_result
[2024-01-24 13:48:16,577] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:16,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:16,604] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:16,604] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:16,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012849095.1_ASM1284909v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:16,605] [INFO] Task started: Blastn
[2024-01-24 13:48:16,605] [INFO] Running command: blastn -query GCF_012849095.1_ASM1284909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa27abc5-8789-4eb8-918f-bf0c2bde3105/dqc_reference/reference_markers_gtdb.fasta -out GCF_012849095.1_ASM1284909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:17,370] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:17,374] [INFO] Selected 14 target genomes.
[2024-01-24 13:48:17,375] [INFO] Target genome list was writen to GCF_012849095.1_ASM1284909v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:17,402] [INFO] Task started: fastANI
[2024-01-24 13:48:17,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a8564f3-463e-4d3e-833d-59c0e4f041e1/GCF_012849095.1_ASM1284909v1_genomic.fna.gz --refList GCF_012849095.1_ASM1284909v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012849095.1_ASM1284909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:34,744] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:34,767] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:34,767] [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_012849095.1	s__Cohnella sp012849095	100.0	2838	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014107495.1	s__Cohnella sp014107495	81.3371	1065	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564235.1	s__Cohnella luojiensis	80.0659	660	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628305.1	s__Cohnella endophytica	80.0136	718	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386205.1	s__Cohnella lupini	79.8986	735	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295585.1	s__Cohnella abietis	79.4677	520	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007786475.1	s__Cohnella terricola	79.1432	597	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386235.1	s__Cohnella phaseoli	78.8	662	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	97.76	97.76	0.83	0.83	2	-
GCF_003001675.1	s__Cohnella sp003001675	78.6867	710	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017874175.1	s__Cohnella suwonensis	78.6405	551	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016424485.1	s__Paenibacillus_D sp016424485	77.9908	89	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829465.1	s__Cohnella kolymensis	77.9531	250	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758665.1	s__Paenibacillus borealis	77.917	90	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005577435.1	s__Paenibacillus sp005577435	77.7671	55	2840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.84	98.84	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:34,769] [INFO] GTDB search result was written to GCF_012849095.1_ASM1284909v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:34,770] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:34,773] [INFO] DFAST_QC result json was written to GCF_012849095.1_ASM1284909v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:34,773] [INFO] DFAST_QC completed!
[2024-01-24 13:48:34,773] [INFO] Total running time: 0h2m5s