[2024-01-24 13:36:56,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:56,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:56,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg4caa141c-bee6-436b-b116-c058572952e4/dqc_reference
[2024-01-24 13:36:57,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:57,918] [INFO] Task started: Prodigal
[2024-01-24 13:36:57,918] [INFO] Running command: gunzip -c /var/lib/cwl/stgdeb12f70-a210-4deb-8a16-086b1ce31652/GCF_022352055.1_ASM2235205v1_genomic.fna.gz | prodigal -d GCF_022352055.1_ASM2235205v1_genomic.fna/cds.fna -a GCF_022352055.1_ASM2235205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:13,875] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:13,876] [INFO] Task started: HMMsearch
[2024-01-24 13:37:13,876] [INFO] Running command: hmmsearch --tblout GCF_022352055.1_ASM2235205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4caa141c-bee6-436b-b116-c058572952e4/dqc_reference/reference_markers.hmm GCF_022352055.1_ASM2235205v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:14,360] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:14,361] [INFO] Found 6/6 markers.
[2024-01-24 13:37:14,413] [INFO] Query marker FASTA was written to GCF_022352055.1_ASM2235205v1_genomic.fna/markers.fasta
[2024-01-24 13:37:14,413] [INFO] Task started: Blastn
[2024-01-24 13:37:14,413] [INFO] Running command: blastn -query GCF_022352055.1_ASM2235205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4caa141c-bee6-436b-b116-c058572952e4/dqc_reference/reference_markers.fasta -out GCF_022352055.1_ASM2235205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:15,062] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:15,065] [INFO] Selected 15 target genomes.
[2024-01-24 13:37:15,066] [INFO] Target genome list was writen to GCF_022352055.1_ASM2235205v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:15,073] [INFO] Task started: fastANI
[2024-01-24 13:37:15,074] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeb12f70-a210-4deb-8a16-086b1ce31652/GCF_022352055.1_ASM2235205v1_genomic.fna.gz --refList GCF_022352055.1_ASM2235205v1_genomic.fna/target_genomes.txt --output GCF_022352055.1_ASM2235205v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:32,144] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:32,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4caa141c-bee6-436b-b116-c058572952e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:32,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4caa141c-bee6-436b-b116-c058572952e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:32,157] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:32,157] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:32,157] [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	83.3783	1239	1915	95	below_threshold
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	81.5861	990	1915	95	below_threshold
Cohnella terricola	strain=G13	GCA_007786475.1	1289167	1289167	type	True	80.1382	549	1915	95	below_threshold
Cohnella luojiensis	strain=CCTCC AB 208254	GCA_004564235.1	652876	652876	type	True	80.0674	574	1915	95	below_threshold
Cohnella endophytica	strain=M2MS4P-1	GCA_003628305.1	2419778	2419778	type	True	79.6457	624	1915	95	below_threshold
Cohnella lupini	strain=CECT 8236	GCA_003386205.1	1294267	1294267	type	True	79.579	600	1915	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	78.0028	223	1915	95	below_threshold
Cohnella panacarvi	strain=Gsoil 349	GCA_000515335.1	400776	400776	type	True	77.9052	306	1915	95	below_threshold
Cohnella kolymensis	strain=VKM B-2846	GCA_000829465.1	1590652	1590652	type	True	77.7827	223	1915	95	below_threshold
Gorillibacterium massiliense	strain=G5	GCA_000455485.2	1280390	1280390	type	True	77.1162	74	1915	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	76.3942	60	1915	95	below_threshold
Gorillibacterium timonense	strain=SN4	GCA_001457415.1	1689269	1689269	type	True	76.3843	50	1915	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	75.9732	74	1915	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	75.8926	67	1915	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:32,159] [INFO] DFAST Taxonomy check result was written to GCF_022352055.1_ASM2235205v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:32,159] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:32,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:32,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4caa141c-bee6-436b-b116-c058572952e4/dqc_reference/checkm_data
[2024-01-24 13:37:32,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:32,217] [INFO] Task started: CheckM
[2024-01-24 13:37:32,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022352055.1_ASM2235205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022352055.1_ASM2235205v1_genomic.fna/checkm_input GCF_022352055.1_ASM2235205v1_genomic.fna/checkm_result
[2024-01-24 13:38:17,751] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:17,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:17,775] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:17,775] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:17,776] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022352055.1_ASM2235205v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:17,776] [INFO] Task started: Blastn
[2024-01-24 13:38:17,776] [INFO] Running command: blastn -query GCF_022352055.1_ASM2235205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4caa141c-bee6-436b-b116-c058572952e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_022352055.1_ASM2235205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:18,578] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:18,583] [INFO] Selected 12 target genomes.
[2024-01-24 13:38:18,583] [INFO] Target genome list was writen to GCF_022352055.1_ASM2235205v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:18,599] [INFO] Task started: fastANI
[2024-01-24 13:38:18,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeb12f70-a210-4deb-8a16-086b1ce31652/GCF_022352055.1_ASM2235205v1_genomic.fna.gz --refList GCF_022352055.1_ASM2235205v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022352055.1_ASM2235205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:31,730] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:31,744] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:38:31,745] [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	83.3871	1238	1915	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	81.6092	986	1915	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	80.0766	573	1915	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	79.6466	623	1915	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	79.5958	597	1915	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	78.887	507	1915	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	78.253	529	1915	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014212125.1	s__Cohnella nanjingensis	78.0028	223	1915	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	77.9037	306	1915	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829465.1	s__Cohnella kolymensis	77.7827	223	1915	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455485.1	s__Gorillibacterium massiliense	77.1162	74	1915	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Gorillibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457415.1	s__Gorillibacterium timonense	76.3843	50	1915	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Gorillibacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:31,746] [INFO] GTDB search result was written to GCF_022352055.1_ASM2235205v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:31,747] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:31,752] [INFO] DFAST_QC result json was written to GCF_022352055.1_ASM2235205v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:31,753] [INFO] DFAST_QC completed!
[2024-01-24 13:38:31,753] [INFO] Total running time: 0h1m35s