[2024-01-24 13:01:49,697] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:49,698] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:49,699] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f8e1c5a-9e34-4a08-910e-96bda2ed398f/dqc_reference
[2024-01-24 13:01:51,120] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:51,124] [INFO] Task started: Prodigal
[2024-01-24 13:01:51,125] [INFO] Running command: gunzip -c /var/lib/cwl/stgc931060d-428a-4a26-a09a-0e34c05e6b33/GCF_000423705.1_ASM42370v1_genomic.fna.gz | prodigal -d GCF_000423705.1_ASM42370v1_genomic.fna/cds.fna -a GCF_000423705.1_ASM42370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:05,297] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:05,298] [INFO] Task started: HMMsearch
[2024-01-24 13:02:05,298] [INFO] Running command: hmmsearch --tblout GCF_000423705.1_ASM42370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f8e1c5a-9e34-4a08-910e-96bda2ed398f/dqc_reference/reference_markers.hmm GCF_000423705.1_ASM42370v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:05,668] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:05,669] [INFO] Found 6/6 markers.
[2024-01-24 13:02:05,718] [INFO] Query marker FASTA was written to GCF_000423705.1_ASM42370v1_genomic.fna/markers.fasta
[2024-01-24 13:02:05,718] [INFO] Task started: Blastn
[2024-01-24 13:02:05,718] [INFO] Running command: blastn -query GCF_000423705.1_ASM42370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f8e1c5a-9e34-4a08-910e-96bda2ed398f/dqc_reference/reference_markers.fasta -out GCF_000423705.1_ASM42370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:06,772] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:06,775] [INFO] Selected 18 target genomes.
[2024-01-24 13:02:06,776] [INFO] Target genome list was writen to GCF_000423705.1_ASM42370v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:06,783] [INFO] Task started: fastANI
[2024-01-24 13:02:06,783] [INFO] Running command: fastANI --query /var/lib/cwl/stgc931060d-428a-4a26-a09a-0e34c05e6b33/GCF_000423705.1_ASM42370v1_genomic.fna.gz --refList GCF_000423705.1_ASM42370v1_genomic.fna/target_genomes.txt --output GCF_000423705.1_ASM42370v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:23,478] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:23,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f8e1c5a-9e34-4a08-910e-96bda2ed398f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:23,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f8e1c5a-9e34-4a08-910e-96bda2ed398f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:23,494] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:23,494] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:23,494] [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
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	100.0	1533	1536	95	conclusive
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	80.6394	793	1536	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	80.6159	800	1536	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	78.8391	557	1536	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	78.4091	410	1536	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	78.3134	436	1536	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	78.1681	424	1536	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	78.1491	400	1536	95	below_threshold
Breoghania corrubedonensis	strain=DSM 23382	GCA_003053845.1	665038	665038	type	True	78.1116	430	1536	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	77.9624	388	1536	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	77.9215	396	1536	95	below_threshold
Roseibium suaedae	strain=DSM 22153	GCA_900142725.1	735517	735517	type	True	77.8425	310	1536	95	below_threshold
Martelella mediterranea	strain=MACL11	GCA_002043005.1	293089	293089	type	True	77.3471	270	1536	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.2184	225	1536	95	below_threshold
Martelella mediterranea	strain=DSM 17316	GCA_000376125.1	293089	293089	type	True	77.1598	264	1536	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	76.9509	221	1536	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	76.6077	282	1536	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.277	200	1536	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:23,497] [INFO] DFAST Taxonomy check result was written to GCF_000423705.1_ASM42370v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:23,498] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:23,498] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:23,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f8e1c5a-9e34-4a08-910e-96bda2ed398f/dqc_reference/checkm_data
[2024-01-24 13:02:23,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:23,547] [INFO] Task started: CheckM
[2024-01-24 13:02:23,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423705.1_ASM42370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423705.1_ASM42370v1_genomic.fna/checkm_input GCF_000423705.1_ASM42370v1_genomic.fna/checkm_result
[2024-01-24 13:03:14,656] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:14,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:14,680] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:14,681] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:14,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423705.1_ASM42370v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:14,682] [INFO] Task started: Blastn
[2024-01-24 13:03:14,682] [INFO] Running command: blastn -query GCF_000423705.1_ASM42370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f8e1c5a-9e34-4a08-910e-96bda2ed398f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423705.1_ASM42370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:16,777] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:16,781] [INFO] Selected 10 target genomes.
[2024-01-24 13:03:16,781] [INFO] Target genome list was writen to GCF_000423705.1_ASM42370v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:16,790] [INFO] Task started: fastANI
[2024-01-24 13:03:16,790] [INFO] Running command: fastANI --query /var/lib/cwl/stgc931060d-428a-4a26-a09a-0e34c05e6b33/GCF_000423705.1_ASM42370v1_genomic.fna.gz --refList GCF_000423705.1_ASM42370v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423705.1_ASM42370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:27,605] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:27,624] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:27,624] [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_000423705.1	s__Stappia stellulata	100.0	1534	1536	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002709505.1	s__Stappia sp002709505	87.6719	1065	1536	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016774605.1	s__Stappia sp016774605	87.0003	1062	1536	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105595.1	s__Stappia sp900105595	86.7888	1229	1536	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789575.1	s__Stappia indica_A	80.7938	899	1536	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185725.1	s__Stappia sp900185725	80.7829	837	1536	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCF_001696535.1	s__Stappia indica	80.7729	881	1536	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_014635285.1	s__Stappia taiwanensis	80.6261	798	1536	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003610575.1	s__Stappia sp003610575	80.5896	868	1536	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCA_002722295.1	s__Stappia sp002722295	79.9678	679	1536	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	99.88	99.88	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:27,627] [INFO] GTDB search result was written to GCF_000423705.1_ASM42370v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:27,627] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:27,631] [INFO] DFAST_QC result json was written to GCF_000423705.1_ASM42370v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:27,631] [INFO] DFAST_QC completed!
[2024-01-24 13:03:27,632] [INFO] Total running time: 0h1m38s