[2023-06-29 16:30:21,539] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:30:21,542] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:30:21,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c7cc31e-704b-4832-b77e-67c1f9c60b0b/dqc_reference
[2023-06-29 16:30:22,913] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:30:22,914] [INFO] Task started: Prodigal
[2023-06-29 16:30:22,914] [INFO] Running command: gunzip -c /var/lib/cwl/stgec87110c-b6d7-45ff-b8b6-a807db9678e3/GCA_021808585.1_ASM2180858v1_genomic.fna.gz | prodigal -d GCA_021808585.1_ASM2180858v1_genomic.fna/cds.fna -a GCA_021808585.1_ASM2180858v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:30:41,344] [INFO] Task succeeded: Prodigal
[2023-06-29 16:30:41,344] [INFO] Task started: HMMsearch
[2023-06-29 16:30:41,344] [INFO] Running command: hmmsearch --tblout GCA_021808585.1_ASM2180858v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c7cc31e-704b-4832-b77e-67c1f9c60b0b/dqc_reference/reference_markers.hmm GCA_021808585.1_ASM2180858v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:30:41,826] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:30:41,828] [INFO] Found 6/6 markers.
[2023-06-29 16:30:41,930] [INFO] Query marker FASTA was written to GCA_021808585.1_ASM2180858v1_genomic.fna/markers.fasta
[2023-06-29 16:30:41,931] [INFO] Task started: Blastn
[2023-06-29 16:30:41,931] [INFO] Running command: blastn -query GCA_021808585.1_ASM2180858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c7cc31e-704b-4832-b77e-67c1f9c60b0b/dqc_reference/reference_markers.fasta -out GCA_021808585.1_ASM2180858v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:30:42,726] [INFO] Task succeeded: Blastn
[2023-06-29 16:30:42,731] [INFO] Selected 33 target genomes.
[2023-06-29 16:30:42,731] [INFO] Target genome list was writen to GCA_021808585.1_ASM2180858v1_genomic.fna/target_genomes.txt
[2023-06-29 16:30:42,739] [INFO] Task started: fastANI
[2023-06-29 16:30:42,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgec87110c-b6d7-45ff-b8b6-a807db9678e3/GCA_021808585.1_ASM2180858v1_genomic.fna.gz --refList GCA_021808585.1_ASM2180858v1_genomic.fna/target_genomes.txt --output GCA_021808585.1_ASM2180858v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:31:06,005] [INFO] Task succeeded: fastANI
[2023-06-29 16:31:06,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c7cc31e-704b-4832-b77e-67c1f9c60b0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:31:06,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c7cc31e-704b-4832-b77e-67c1f9c60b0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:31:06,013] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:31:06,014] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:31:06,014] [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
Rhizomicrobium palustre	strain=DSM 19867	GCA_011761565.1	189966	189966	type	True	76.5064	59	1995	95	below_threshold
Rhizomicrobium electricum	strain=DSM 21034	GCA_011762045.1	480070	480070	type	True	75.936	74	1995	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	75.4528	54	1995	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_019684455.1	1138190	1138190	type	True	75.4357	55	1995	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	75.0961	56	1995	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	74.8603	52	1995	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:31:06,016] [INFO] DFAST Taxonomy check result was written to GCA_021808585.1_ASM2180858v1_genomic.fna/tc_result.tsv
[2023-06-29 16:31:06,017] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:31:06,017] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:31:06,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c7cc31e-704b-4832-b77e-67c1f9c60b0b/dqc_reference/checkm_data
[2023-06-29 16:31:06,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:31:06,084] [INFO] Task started: CheckM
[2023-06-29 16:31:06,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021808585.1_ASM2180858v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021808585.1_ASM2180858v1_genomic.fna/checkm_input GCA_021808585.1_ASM2180858v1_genomic.fna/checkm_result
[2023-06-29 16:31:59,144] [INFO] Task succeeded: CheckM
[2023-06-29 16:31:59,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:31:59,171] [INFO] ===== Completeness check finished =====
[2023-06-29 16:31:59,171] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:31:59,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021808585.1_ASM2180858v1_genomic.fna/markers.fasta)
[2023-06-29 16:31:59,172] [INFO] Task started: Blastn
[2023-06-29 16:31:59,172] [INFO] Running command: blastn -query GCA_021808585.1_ASM2180858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c7cc31e-704b-4832-b77e-67c1f9c60b0b/dqc_reference/reference_markers_gtdb.fasta -out GCA_021808585.1_ASM2180858v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:32:00,338] [INFO] Task succeeded: Blastn
[2023-06-29 16:32:00,343] [INFO] Selected 29 target genomes.
[2023-06-29 16:32:00,343] [INFO] Target genome list was writen to GCA_021808585.1_ASM2180858v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:32:00,369] [INFO] Task started: fastANI
[2023-06-29 16:32:00,370] [INFO] Running command: fastANI --query /var/lib/cwl/stgec87110c-b6d7-45ff-b8b6-a807db9678e3/GCA_021808585.1_ASM2180858v1_genomic.fna.gz --refList GCA_021808585.1_ASM2180858v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021808585.1_ASM2180858v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:32:16,084] [INFO] Task succeeded: fastANI
[2023-06-29 16:32:16,103] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:32:16,103] [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_902712915.1	s__Acidiphilium sp002255515	78.0347	83	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	99.59	99.19	0.97	0.94	3	-
GCA_018971835.1	s__Rhizomicrobium sp018971835	77.2049	120	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308375.1	s__Rhizomicrobium sp001898015	76.5419	92	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	98.73	97.98	0.95	0.90	6	-
GCF_011761565.1	s__Rhizomicrobium palustre	76.5412	58	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019245415.1	s__Rhizomicrobium sp019245415	76.4357	85	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	99.94	99.94	0.99	0.99	2	-
GCA_018970685.1	s__Rhizomicrobium sp018970685	76.3961	51	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825865.1	s__Rhizomicrobium sp902825865	76.366	66	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018449595.1	s__Rhizomicrobium sp018449595	76.2373	75	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837555.1	s__Rhizomicrobium sp903837555	76.1888	58	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307355.1	s__Rhizomicrobium sp017307355	76.17	67	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242145.1	s__Rhizomicrobium sp018242145	76.151	74	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003139615.1	s__Rhizomicrobium sp003139615	76.0476	68	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	96.56	95.41	0.83	0.78	5	-
GCF_011762045.1	s__Rhizomicrobium electricum	75.936	74	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016783965.1	s__Rhizomicrobium sp016783965	75.8797	71	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	99.99	99.98	0.99	0.99	3	-
GCF_013149165.1	s__Rhizomicrobium sp013149165	75.8146	66	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654705.1	s__Rhizomicrobium sp015654705	75.735	52	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429315.1	s__Rhizomicrobium sp002429315	75.5819	78	1995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	99.86	99.86	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-29 16:32:16,105] [INFO] GTDB search result was written to GCA_021808585.1_ASM2180858v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:32:16,106] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:32:16,110] [INFO] DFAST_QC result json was written to GCA_021808585.1_ASM2180858v1_genomic.fna/dqc_result.json
[2023-06-29 16:32:16,110] [INFO] DFAST_QC completed!
[2023-06-29 16:32:16,110] [INFO] Total running time: 0h1m55s