[2024-01-24 13:17:05,465] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:05,467] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:05,467] [INFO] DQC Reference Directory: /var/lib/cwl/stgb38f99cc-ddb0-418b-859b-9ef0a9a8c633/dqc_reference
[2024-01-24 13:17:06,827] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,828] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,828] [INFO] Running command: gunzip -c /var/lib/cwl/stg041a94c8-5346-42e6-927e-80d1defd17dd/GCF_003570905.1_ASM357090v1_genomic.fna.gz | prodigal -d GCF_003570905.1_ASM357090v1_genomic.fna/cds.fna -a GCF_003570905.1_ASM357090v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:24,306] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:24,306] [INFO] Task started: HMMsearch
[2024-01-24 13:17:24,307] [INFO] Running command: hmmsearch --tblout GCF_003570905.1_ASM357090v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb38f99cc-ddb0-418b-859b-9ef0a9a8c633/dqc_reference/reference_markers.hmm GCF_003570905.1_ASM357090v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:24,695] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:24,696] [INFO] Found 6/6 markers.
[2024-01-24 13:17:24,747] [INFO] Query marker FASTA was written to GCF_003570905.1_ASM357090v1_genomic.fna/markers.fasta
[2024-01-24 13:17:24,748] [INFO] Task started: Blastn
[2024-01-24 13:17:24,748] [INFO] Running command: blastn -query GCF_003570905.1_ASM357090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb38f99cc-ddb0-418b-859b-9ef0a9a8c633/dqc_reference/reference_markers.fasta -out GCF_003570905.1_ASM357090v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:25,368] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:25,372] [INFO] Selected 21 target genomes.
[2024-01-24 13:17:25,372] [INFO] Target genome list was writen to GCF_003570905.1_ASM357090v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:25,380] [INFO] Task started: fastANI
[2024-01-24 13:17:25,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg041a94c8-5346-42e6-927e-80d1defd17dd/GCF_003570905.1_ASM357090v1_genomic.fna.gz --refList GCF_003570905.1_ASM357090v1_genomic.fna/target_genomes.txt --output GCF_003570905.1_ASM357090v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:49,907] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:49,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb38f99cc-ddb0-418b-859b-9ef0a9a8c633/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:49,908] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb38f99cc-ddb0-418b-859b-9ef0a9a8c633/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:49,924] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:49,924] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:49,924] [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 faecalis	strain=K2E09-144	GCA_003570905.1	2315694	2315694	type	True	100.0	2092	2106	95	conclusive
Cohnella candidum	strain=18JY8-7	GCA_003713065.1	2674991	2674991	type	True	78.7741	361	2106	95	below_threshold
Cohnella panacarvi	strain=Gsoil 349	GCA_000515335.1	400776	400776	type	True	78.2641	336	2106	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	78.1493	352	2106	95	below_threshold
Cohnella pontilimi	strain=CAU 1483	GCA_005049045.1	2564100	2564100	type	True	77.9154	278	2106	95	below_threshold
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	77.9079	319	2106	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_014212015.1	2163172	2163172	type	True	77.9076	260	2106	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	77.897	262	2106	95	below_threshold
Cohnella endophytica	strain=M2MS4P-1	GCA_003628305.1	2419778	2419778	type	True	77.8058	331	2106	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	77.7831	375	2106	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	77.6829	343	2106	95	below_threshold
Cohnella thailandensis	strain=DSM 25241	GCA_014212135.1	557557	557557	type	True	77.6774	317	2106	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	77.6358	264	2106	95	below_threshold
Paenibacillus beijingensis	strain=DSM 24997	GCA_000961095.1	1126833	1126833	type	True	77.5048	195	2106	95	below_threshold
Paenibacillus hemerocallicola	strain=KCTC 33185	GCA_006265175.1	1172614	1172614	type	True	77.3386	186	2106	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	76.6294	127	2106	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	76.4859	66	2106	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.3774	105	2106	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	76.3369	99	2106	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	76.3252	82	2106	95	below_threshold
Paenibacillus phytorum	strain=LMG 31458	GCA_013141715.1	2654977	2654977	type	True	76.304	72	2106	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:49,926] [INFO] DFAST Taxonomy check result was written to GCF_003570905.1_ASM357090v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:49,927] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:49,927] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:49,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb38f99cc-ddb0-418b-859b-9ef0a9a8c633/dqc_reference/checkm_data
[2024-01-24 13:17:49,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:49,989] [INFO] Task started: CheckM
[2024-01-24 13:17:49,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003570905.1_ASM357090v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003570905.1_ASM357090v1_genomic.fna/checkm_input GCF_003570905.1_ASM357090v1_genomic.fna/checkm_result
[2024-01-24 13:18:40,716] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:40,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.65%
Contamintation: 14.58%
Strain heterogeneity: 91.67%
--------------------------------------------------------------------------------
[2024-01-24 13:18:40,748] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:40,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:40,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003570905.1_ASM357090v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:40,749] [INFO] Task started: Blastn
[2024-01-24 13:18:40,749] [INFO] Running command: blastn -query GCF_003570905.1_ASM357090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb38f99cc-ddb0-418b-859b-9ef0a9a8c633/dqc_reference/reference_markers_gtdb.fasta -out GCF_003570905.1_ASM357090v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:41,625] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:41,630] [INFO] Selected 17 target genomes.
[2024-01-24 13:18:41,630] [INFO] Target genome list was writen to GCF_003570905.1_ASM357090v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:41,653] [INFO] Task started: fastANI
[2024-01-24 13:18:41,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg041a94c8-5346-42e6-927e-80d1defd17dd/GCF_003570905.1_ASM357090v1_genomic.fna.gz --refList GCF_003570905.1_ASM357090v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003570905.1_ASM357090v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:01,287] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:01,307] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:01,308] [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_003570905.1	s__Cohnella faecalis	100.0	2096	2106	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_003713065.1	s__Cohnella candidum	78.7492	363	2106	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515335.1	s__Cohnella panacarvi	78.281	335	2106	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016937515.1	s__Cohnella algarum	78.2152	331	2106	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.08	99.08	0.87	0.87	3	-
GCF_000429825.1	s__Cohnella thermotolerans	78.1283	349	2106	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	77.9674	383	2106	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	77.9527	409	2106	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005049045.1	s__Cohnella pontilimi	77.9523	275	2106	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	77.9506	318	2106	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212015.1	s__Cohnella lubricantis	77.9265	259	2106	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014212175.1	s__Cohnella xylanilytica	77.7933	374	2106	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_003628305.1	s__Cohnella endophytica	77.7864	332	2106	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990975.1	s__Cohnella sp003990975	77.7779	293	2106	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	77.7302	348	2106	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	97.76	97.76	0.83	0.83	2	-
GCF_006265175.1	s__Paenibacillus_AB hemerocallicola	77.4067	182	2106	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620565.1	s__Paenibacillus_E sp000620565	76.7692	66	2106	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_013204885.1	s__Paenibacillus tritici	76.497	66	2106	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.22	98.22	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:01,309] [INFO] GTDB search result was written to GCF_003570905.1_ASM357090v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:01,310] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:01,314] [INFO] DFAST_QC result json was written to GCF_003570905.1_ASM357090v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:01,315] [INFO] DFAST_QC completed!
[2024-01-24 13:19:01,315] [INFO] Total running time: 0h1m56s