[2024-01-24 14:06:02,846] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:02,849] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:02,849] [INFO] DQC Reference Directory: /var/lib/cwl/stge1d83384-645d-436c-acd2-0fc386bdf030/dqc_reference
[2024-01-24 14:06:04,111] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:04,112] [INFO] Task started: Prodigal
[2024-01-24 14:06:04,113] [INFO] Running command: gunzip -c /var/lib/cwl/stga0ab1616-906c-462d-96b3-19aaa76fb1d8/GCF_004295585.1_ASM429558v1_genomic.fna.gz | prodigal -d GCF_004295585.1_ASM429558v1_genomic.fna/cds.fna -a GCF_004295585.1_ASM429558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:21,728] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:21,729] [INFO] Task started: HMMsearch
[2024-01-24 14:06:21,729] [INFO] Running command: hmmsearch --tblout GCF_004295585.1_ASM429558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1d83384-645d-436c-acd2-0fc386bdf030/dqc_reference/reference_markers.hmm GCF_004295585.1_ASM429558v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:22,099] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:22,100] [INFO] Found 6/6 markers.
[2024-01-24 14:06:22,166] [INFO] Query marker FASTA was written to GCF_004295585.1_ASM429558v1_genomic.fna/markers.fasta
[2024-01-24 14:06:22,167] [INFO] Task started: Blastn
[2024-01-24 14:06:22,167] [INFO] Running command: blastn -query GCF_004295585.1_ASM429558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1d83384-645d-436c-acd2-0fc386bdf030/dqc_reference/reference_markers.fasta -out GCF_004295585.1_ASM429558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:22,856] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:22,865] [INFO] Selected 14 target genomes.
[2024-01-24 14:06:22,865] [INFO] Target genome list was writen to GCF_004295585.1_ASM429558v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:22,889] [INFO] Task started: fastANI
[2024-01-24 14:06:22,890] [INFO] Running command: fastANI --query /var/lib/cwl/stga0ab1616-906c-462d-96b3-19aaa76fb1d8/GCF_004295585.1_ASM429558v1_genomic.fna.gz --refList GCF_004295585.1_ASM429558v1_genomic.fna/target_genomes.txt --output GCF_004295585.1_ASM429558v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:40,069] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:40,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1d83384-645d-436c-acd2-0fc386bdf030/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:40,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1d83384-645d-436c-acd2-0fc386bdf030/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:40,085] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:40,086] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:40,086] [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 abietis	strain=HS21	GCA_004295585.1	2507935	2507935	type	True	100.0	2353	2353	95	conclusive
Paenibacillus baekrokdamisoli	strain=KCTC 33723	GCA_003945345.1	1712516	1712516	type	True	80.1322	189	2353	95	below_threshold
Cohnella cholangitidis	strain=1605-214	GCA_014107495.1	2598458	2598458	type	True	79.5387	404	2353	95	below_threshold
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	79.4888	505	2353	95	below_threshold
Paenibacillus alvei	strain=DSM 29	GCA_000293805.1	44250	44250	type	True	79.4144	58	2353	95	below_threshold
Cohnella endophytica	strain=M2MS4P-1	GCA_003628305.1	2419778	2419778	type	True	79.2815	387	2353	95	below_threshold
Cohnella luojiensis	strain=CCTCC AB 208254	GCA_004564235.1	652876	652876	type	True	79.2271	423	2353	95	below_threshold
Cohnella lupini	strain=CECT 8236	GCA_003386205.1	1294267	1294267	type	True	79.1875	428	2353	95	below_threshold
Paenibacillus endophyticus	strain=CECT 8234	GCA_014192395.1	1294268	1294268	type	True	78.2571	77	2353	95	below_threshold
Paenibacillus prosopidis	strain=CECT 7506	GCA_003337375.1	630520	630520	type	True	77.3733	67	2353	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	76.9946	94	2353	95	below_threshold
Paenibacillus lupini	strain=CECT 8235	GCA_011761355.1	1450204	1450204	type	True	76.655	83	2353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:40,089] [INFO] DFAST Taxonomy check result was written to GCF_004295585.1_ASM429558v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:40,090] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:40,090] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:40,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1d83384-645d-436c-acd2-0fc386bdf030/dqc_reference/checkm_data
[2024-01-24 14:06:40,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:40,158] [INFO] Task started: CheckM
[2024-01-24 14:06:40,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004295585.1_ASM429558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004295585.1_ASM429558v1_genomic.fna/checkm_input GCF_004295585.1_ASM429558v1_genomic.fna/checkm_result
[2024-01-24 14:07:33,044] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:33,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:33,070] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:33,070] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:33,071] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004295585.1_ASM429558v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:33,071] [INFO] Task started: Blastn
[2024-01-24 14:07:33,071] [INFO] Running command: blastn -query GCF_004295585.1_ASM429558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1d83384-645d-436c-acd2-0fc386bdf030/dqc_reference/reference_markers_gtdb.fasta -out GCF_004295585.1_ASM429558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:33,876] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:33,880] [INFO] Selected 12 target genomes.
[2024-01-24 14:07:33,881] [INFO] Target genome list was writen to GCF_004295585.1_ASM429558v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:33,894] [INFO] Task started: fastANI
[2024-01-24 14:07:33,894] [INFO] Running command: fastANI --query /var/lib/cwl/stga0ab1616-906c-462d-96b3-19aaa76fb1d8/GCF_004295585.1_ASM429558v1_genomic.fna.gz --refList GCF_004295585.1_ASM429558v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004295585.1_ASM429558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:48,218] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:48,234] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:48,234] [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_004295585.1	s__Cohnella abietis	100.0	2353	2353	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	79.4994	403	2353	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849095.1	s__Cohnella sp012849095	79.4941	503	2353	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	79.297	386	2353	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	79.2271	423	2353	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	79.187	429	2353	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741035.1	s__Paenibacillus_C sp002741035	78.996	107	2353	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	95.68	95.68	0.84	0.84	2	-
GCF_017874175.1	s__Cohnella suwonensis	77.9342	237	2353	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	77.6001	281	2353	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	97.76	97.76	0.83	0.83	2	-
GCF_003337375.1	s__Paenibacillus_C prosopidis	77.3729	66	2353	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:48,236] [INFO] GTDB search result was written to GCF_004295585.1_ASM429558v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:48,236] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:48,240] [INFO] DFAST_QC result json was written to GCF_004295585.1_ASM429558v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:48,240] [INFO] DFAST_QC completed!
[2024-01-24 14:07:48,241] [INFO] Total running time: 0h1m45s