[2024-01-24 12:29:36,041] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:36,042] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:36,042] [INFO] DQC Reference Directory: /var/lib/cwl/stg703575d0-df9b-4d2c-b450-c54f68b6548c/dqc_reference
[2024-01-24 12:29:37,330] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:37,335] [INFO] Task started: Prodigal
[2024-01-24 12:29:37,336] [INFO] Running command: gunzip -c /var/lib/cwl/stgf13d4eec-1f58-4ae5-857a-fe90d20e8caf/GCF_029892045.1_ASM2989204v1_genomic.fna.gz | prodigal -d GCF_029892045.1_ASM2989204v1_genomic.fna/cds.fna -a GCF_029892045.1_ASM2989204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:57,232] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:57,233] [INFO] Task started: HMMsearch
[2024-01-24 12:29:57,233] [INFO] Running command: hmmsearch --tblout GCF_029892045.1_ASM2989204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg703575d0-df9b-4d2c-b450-c54f68b6548c/dqc_reference/reference_markers.hmm GCF_029892045.1_ASM2989204v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:57,555] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:57,557] [INFO] Found 6/6 markers.
[2024-01-24 12:29:57,611] [INFO] Query marker FASTA was written to GCF_029892045.1_ASM2989204v1_genomic.fna/markers.fasta
[2024-01-24 12:29:57,612] [INFO] Task started: Blastn
[2024-01-24 12:29:57,612] [INFO] Running command: blastn -query GCF_029892045.1_ASM2989204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg703575d0-df9b-4d2c-b450-c54f68b6548c/dqc_reference/reference_markers.fasta -out GCF_029892045.1_ASM2989204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:58,603] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:58,606] [INFO] Selected 17 target genomes.
[2024-01-24 12:29:58,606] [INFO] Target genome list was writen to GCF_029892045.1_ASM2989204v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:58,612] [INFO] Task started: fastANI
[2024-01-24 12:29:58,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgf13d4eec-1f58-4ae5-857a-fe90d20e8caf/GCF_029892045.1_ASM2989204v1_genomic.fna.gz --refList GCF_029892045.1_ASM2989204v1_genomic.fna/target_genomes.txt --output GCF_029892045.1_ASM2989204v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:21,052] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:21,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg703575d0-df9b-4d2c-b450-c54f68b6548c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:21,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg703575d0-df9b-4d2c-b450-c54f68b6548c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:21,069] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:30:21,069] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:30:21,069] [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
Ensifer psoraleae	strain=CCBAU 65732	GCA_013283645.1	520838	520838	type	True	83.3759	1382	2239	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	83.1728	1264	2239	95	below_threshold
Sinorhizobium fredii	strain=USDA205	GCA_009601405.1	380	380	type	True	83.158	1335	2239	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	83.0877	1293	2239	95	below_threshold
Ensifer mexicanus	strain=DSM 18446	GCA_017873105.1	375549	375549	type	True	82.8341	1264	2239	95	below_threshold
Ensifer mexicanus	strain=ITTG R7	GCA_013488225.1	375549	375549	type	True	82.8326	1263	2239	95	below_threshold
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	82.4499	1198	2239	95	below_threshold
Sinorhizobium meliloti	strain=USDA 1002	GCA_017876815.1	382	382	type	True	82.4243	1305	2239	95	below_threshold
Sinorhizobium meliloti	strain=USDA1002	GCA_009601385.1	382	382	type	True	82.3799	1250	2239	95	below_threshold
Sinorhizobium kostiense	strain=DSM 13372	GCA_017874595.1	76747	76747	type	True	82.2953	1188	2239	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	82.2304	1146	2239	95	below_threshold
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	81.5971	1099	2239	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.9139	709	2239	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.5091	666	2239	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	79.1684	546	2239	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	79.0004	705	2239	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	78.6229	684	2239	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:21,072] [INFO] DFAST Taxonomy check result was written to GCF_029892045.1_ASM2989204v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:21,072] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:21,073] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:21,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg703575d0-df9b-4d2c-b450-c54f68b6548c/dqc_reference/checkm_data
[2024-01-24 12:30:21,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:21,136] [INFO] Task started: CheckM
[2024-01-24 12:30:21,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_029892045.1_ASM2989204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_029892045.1_ASM2989204v1_genomic.fna/checkm_input GCF_029892045.1_ASM2989204v1_genomic.fna/checkm_result
[2024-01-24 12:31:18,275] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:18,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:18,322] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:18,323] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:18,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_029892045.1_ASM2989204v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:18,324] [INFO] Task started: Blastn
[2024-01-24 12:31:18,324] [INFO] Running command: blastn -query GCF_029892045.1_ASM2989204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg703575d0-df9b-4d2c-b450-c54f68b6548c/dqc_reference/reference_markers_gtdb.fasta -out GCF_029892045.1_ASM2989204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:20,299] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:20,305] [INFO] Selected 19 target genomes.
[2024-01-24 12:31:20,306] [INFO] Target genome list was writen to GCF_029892045.1_ASM2989204v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:20,327] [INFO] Task started: fastANI
[2024-01-24 12:31:20,328] [INFO] Running command: fastANI --query /var/lib/cwl/stgf13d4eec-1f58-4ae5-857a-fe90d20e8caf/GCF_029892045.1_ASM2989204v1_genomic.fna.gz --refList GCF_029892045.1_ASM2989204v1_genomic.fna/target_genomes_gtdb.txt --output GCF_029892045.1_ASM2989204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:48,563] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:48,590] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:31:48,591] [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_001651875.1	s__Sinorhizobium saheli	83.4388	1233	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.97	99.97	0.96	0.96	2	-
GCA_001704765.1	s__Sinorhizobium shofinae	83.4027	1181	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078505.1	s__Sinorhizobium aridi	83.3957	1456	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.86	98.54	0.86	0.82	7	-
GCF_013283645.1	s__Sinorhizobium psoraleae	83.3745	1381	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513895.1	s__Sinorhizobium sp000513895	83.3477	1404	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265205.3	s__Sinorhizobium fredii_B	83.2914	1408	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.03	98.03	0.83	0.83	2	-
GCF_001651865.1	s__Sinorhizobium glycinis	83.201	1287	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001461695.1	s__Sinorhizobium fredii	83.0987	1292	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.55	96.82	0.88	0.82	17	-
GCF_000018545.1	s__Sinorhizobium fredii_A	83.0854	1344	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004827385.1	s__Sinorhizobium sp004827385	82.97	1397	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002944405.1	s__Sinorhizobium fredii_C	82.9517	1306	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.60	98.35	0.89	0.83	7	-
GCF_000378985.1	s__Sinorhizobium sp000378985	82.9494	1326	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013488225.1	s__Sinorhizobium mexicanum	82.8512	1266	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001651855.1	s__Sinorhizobium americanum	82.8497	1270	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.81	98.12	0.92	0.85	4	-
GCF_009601505.1	s__Sinorhizobium terangae	82.7596	1344	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_002288525.1	s__Sinorhizobium sojae	82.3072	1178	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017874595.1	s__Sinorhizobium kostiense	82.2736	1190	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283665.1	s__Ensifer sesbaniae	81.6027	1095	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.93	98.93	0.89	0.89	2	-
GCF_002007205.1	s__Ensifer adhaerens_D	81.3792	1048	2239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:48,593] [INFO] GTDB search result was written to GCF_029892045.1_ASM2989204v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:48,593] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:48,597] [INFO] DFAST_QC result json was written to GCF_029892045.1_ASM2989204v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:48,597] [INFO] DFAST_QC completed!
[2024-01-24 12:31:48,598] [INFO] Total running time: 0h2m13s