[2024-01-24 11:05:21,437] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:21,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:21,439] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd232a6a-b6f1-4ed4-a5bf-922154a48ed6/dqc_reference
[2024-01-24 11:05:22,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:22,664] [INFO] Task started: Prodigal
[2024-01-24 11:05:22,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg179b2867-ebe8-4ae0-962c-530686ed180f/GCF_014107495.1_ASM1410749v1_genomic.fna.gz | prodigal -d GCF_014107495.1_ASM1410749v1_genomic.fna/cds.fna -a GCF_014107495.1_ASM1410749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:40,386] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:40,386] [INFO] Task started: HMMsearch
[2024-01-24 11:05:40,386] [INFO] Running command: hmmsearch --tblout GCF_014107495.1_ASM1410749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd232a6a-b6f1-4ed4-a5bf-922154a48ed6/dqc_reference/reference_markers.hmm GCF_014107495.1_ASM1410749v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:40,771] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:40,772] [INFO] Found 6/6 markers.
[2024-01-24 11:05:40,826] [INFO] Query marker FASTA was written to GCF_014107495.1_ASM1410749v1_genomic.fna/markers.fasta
[2024-01-24 11:05:40,827] [INFO] Task started: Blastn
[2024-01-24 11:05:40,827] [INFO] Running command: blastn -query GCF_014107495.1_ASM1410749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd232a6a-b6f1-4ed4-a5bf-922154a48ed6/dqc_reference/reference_markers.fasta -out GCF_014107495.1_ASM1410749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:41,458] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:41,461] [INFO] Selected 16 target genomes.
[2024-01-24 11:05:41,462] [INFO] Target genome list was writen to GCF_014107495.1_ASM1410749v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:41,476] [INFO] Task started: fastANI
[2024-01-24 11:05:41,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg179b2867-ebe8-4ae0-962c-530686ed180f/GCF_014107495.1_ASM1410749v1_genomic.fna.gz --refList GCF_014107495.1_ASM1410749v1_genomic.fna/target_genomes.txt --output GCF_014107495.1_ASM1410749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:00,381] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:00,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd232a6a-b6f1-4ed4-a5bf-922154a48ed6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:00,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd232a6a-b6f1-4ed4-a5bf-922154a48ed6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:00,394] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:00,395] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:00,395] [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 cholangitidis	strain=1605-214	GCA_014107495.1	2598458	2598458	type	True	100.0	2136	2136	95	conclusive
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	81.4174	1039	2136	95	below_threshold
Cohnella luojiensis	strain=CCTCC AB 208254	GCA_004564235.1	652876	652876	type	True	80.0939	608	2136	95	below_threshold
Cohnella lupini	strain=CECT 8236	GCA_003386205.1	1294267	1294267	type	True	79.8624	645	2136	95	below_threshold
Cohnella endophytica	strain=M2MS4P-1	GCA_003628305.1	2419778	2419778	type	True	79.6147	633	2136	95	below_threshold
Cohnella terricola	strain=G13	GCA_007786475.1	1289167	1289167	type	True	79.1965	565	2136	95	below_threshold
Cohnella panacarvi	strain=Gsoil 349	GCA_000515335.1	400776	400776	type	True	78.3244	367	2136	95	below_threshold
Paenibacillus nasutitermitis	strain=CGMCC 1.15178	GCA_014641075.1	1652958	1652958	type	True	77.7939	117	2136	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	77.5585	67	2136	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.9672	100	2136	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	76.7401	73	2136	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.5528	93	2136	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.3271	106	2136	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:00,397] [INFO] DFAST Taxonomy check result was written to GCF_014107495.1_ASM1410749v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:00,401] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:00,401] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:00,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd232a6a-b6f1-4ed4-a5bf-922154a48ed6/dqc_reference/checkm_data
[2024-01-24 11:06:00,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:00,472] [INFO] Task started: CheckM
[2024-01-24 11:06:00,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014107495.1_ASM1410749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014107495.1_ASM1410749v1_genomic.fna/checkm_input GCF_014107495.1_ASM1410749v1_genomic.fna/checkm_result
[2024-01-24 11:06:52,191] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:52,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:52,217] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:52,217] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:52,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014107495.1_ASM1410749v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:52,218] [INFO] Task started: Blastn
[2024-01-24 11:06:52,218] [INFO] Running command: blastn -query GCF_014107495.1_ASM1410749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd232a6a-b6f1-4ed4-a5bf-922154a48ed6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014107495.1_ASM1410749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:53,032] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:53,036] [INFO] Selected 14 target genomes.
[2024-01-24 11:06:53,037] [INFO] Target genome list was writen to GCF_014107495.1_ASM1410749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:53,065] [INFO] Task started: fastANI
[2024-01-24 11:06:53,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg179b2867-ebe8-4ae0-962c-530686ed180f/GCF_014107495.1_ASM1410749v1_genomic.fna.gz --refList GCF_014107495.1_ASM1410749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014107495.1_ASM1410749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:08,985] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:08,996] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:08,996] [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_014107495.1	s__Cohnella sp014107495	100.0	2135	2136	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_012849095.1	s__Cohnella sp012849095	81.419	1034	2136	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	80.0903	607	2136	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	79.8625	645	2136	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	79.6065	634	2136	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908615.1	s__Cohnella boryungensis	79.3513	610	2136	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874175.1	s__Cohnella suwonensis	79.0476	545	2136	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001675.1	s__Cohnella sp003001675	78.7344	610	2136	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000515335.1	s__Cohnella panacarvi	78.3283	366	2136	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013141695.1	s__Paenibacillus_E plantarum	78.0732	62	2136	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829455.1	s__VKM-B-2647 sp000829455	76.8602	118	2136	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__VKM-B-2647	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003854965.1	s__Paenibacillus sp003854965	76.5677	93	2136	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.02	95.02	0.86	0.86	2	-
GCF_009725165.1	s__Paenibacillus_A woosongensis	76.3782	77	2136	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	95.99	95.99	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:08,998] [INFO] GTDB search result was written to GCF_014107495.1_ASM1410749v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:08,998] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:09,002] [INFO] DFAST_QC result json was written to GCF_014107495.1_ASM1410749v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:09,002] [INFO] DFAST_QC completed!
[2024-01-24 11:07:09,002] [INFO] Total running time: 0h1m48s