[2023-06-30 20:55:02,005] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:55:02,011] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:55:02,011] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a770ddb-71a6-458c-9149-645caa2a507b/dqc_reference
[2023-06-30 20:55:04,479] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:55:04,480] [INFO] Task started: Prodigal
[2023-06-30 20:55:04,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg36a3f70d-a9eb-4627-954d-3ab9c9485407/GCA_024642425.1_ASM2464242v1_genomic.fna.gz | prodigal -d GCA_024642425.1_ASM2464242v1_genomic.fna/cds.fna -a GCA_024642425.1_ASM2464242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:55:10,805] [INFO] Task succeeded: Prodigal
[2023-06-30 20:55:10,806] [INFO] Task started: HMMsearch
[2023-06-30 20:55:10,806] [INFO] Running command: hmmsearch --tblout GCA_024642425.1_ASM2464242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a770ddb-71a6-458c-9149-645caa2a507b/dqc_reference/reference_markers.hmm GCA_024642425.1_ASM2464242v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:55:11,057] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:55:11,058] [INFO] Found 6/6 markers.
[2023-06-30 20:55:11,083] [INFO] Query marker FASTA was written to GCA_024642425.1_ASM2464242v1_genomic.fna/markers.fasta
[2023-06-30 20:55:11,083] [INFO] Task started: Blastn
[2023-06-30 20:55:11,084] [INFO] Running command: blastn -query GCA_024642425.1_ASM2464242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a770ddb-71a6-458c-9149-645caa2a507b/dqc_reference/reference_markers.fasta -out GCA_024642425.1_ASM2464242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:55:11,725] [INFO] Task succeeded: Blastn
[2023-06-30 20:55:11,730] [INFO] Selected 25 target genomes.
[2023-06-30 20:55:11,731] [INFO] Target genome list was writen to GCA_024642425.1_ASM2464242v1_genomic.fna/target_genomes.txt
[2023-06-30 20:55:11,762] [INFO] Task started: fastANI
[2023-06-30 20:55:11,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg36a3f70d-a9eb-4627-954d-3ab9c9485407/GCA_024642425.1_ASM2464242v1_genomic.fna.gz --refList GCA_024642425.1_ASM2464242v1_genomic.fna/target_genomes.txt --output GCA_024642425.1_ASM2464242v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:55:26,906] [INFO] Task succeeded: fastANI
[2023-06-30 20:55:26,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a770ddb-71a6-458c-9149-645caa2a507b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:55:26,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a770ddb-71a6-458c-9149-645caa2a507b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:55:26,922] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 20:55:26,922] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 20:55:26,922] [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
Fluviibacter phosphoraccumulans	strain=SHINM1	GCA_016110345.1	1751046	1751046	type	True	98.7468	622	690	95	conclusive
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	77.7651	83	690	95	below_threshold
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	77.4453	86	690	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	77.2625	85	690	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	77.2488	91	690	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	76.8409	81	690	95	below_threshold
Zoogloea dura	strain=G-4-1-14	GCA_012927165.1	2728840	2728840	type	True	76.6092	71	690	95	below_threshold
Pandoraea pulmonicola	strain=DSM 16583	GCA_000815105.2	93221	93221	type	True	76.5234	51	690	95	below_threshold
Pandoraea pulmonicola	strain=NCTC13159	GCA_900454575.1	93221	93221	type	True	76.481	50	690	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	76.3205	83	690	95	below_threshold
Propionivibrio limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	76.3085	52	690	95	below_threshold
Azospira inquinata	strain=Azo-3	GCA_018905915.1	2785627	2785627	type	True	76.1202	55	690	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:55:26,925] [INFO] DFAST Taxonomy check result was written to GCA_024642425.1_ASM2464242v1_genomic.fna/tc_result.tsv
[2023-06-30 20:55:26,925] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:55:26,926] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:55:26,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a770ddb-71a6-458c-9149-645caa2a507b/dqc_reference/checkm_data
[2023-06-30 20:55:26,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:55:26,951] [INFO] Task started: CheckM
[2023-06-30 20:55:26,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024642425.1_ASM2464242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024642425.1_ASM2464242v1_genomic.fna/checkm_input GCA_024642425.1_ASM2464242v1_genomic.fna/checkm_result
[2023-06-30 20:55:51,639] [INFO] Task succeeded: CheckM
[2023-06-30 20:55:51,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:55:51,662] [INFO] ===== Completeness check finished =====
[2023-06-30 20:55:51,663] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:55:51,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024642425.1_ASM2464242v1_genomic.fna/markers.fasta)
[2023-06-30 20:55:51,663] [INFO] Task started: Blastn
[2023-06-30 20:55:51,664] [INFO] Running command: blastn -query GCA_024642425.1_ASM2464242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a770ddb-71a6-458c-9149-645caa2a507b/dqc_reference/reference_markers_gtdb.fasta -out GCA_024642425.1_ASM2464242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:55:52,590] [INFO] Task succeeded: Blastn
[2023-06-30 20:55:52,595] [INFO] Selected 17 target genomes.
[2023-06-30 20:55:52,595] [INFO] Target genome list was writen to GCA_024642425.1_ASM2464242v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:55:52,604] [INFO] Task started: fastANI
[2023-06-30 20:55:52,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg36a3f70d-a9eb-4627-954d-3ab9c9485407/GCA_024642425.1_ASM2464242v1_genomic.fna.gz --refList GCA_024642425.1_ASM2464242v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024642425.1_ASM2464242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:56:01,551] [INFO] Task succeeded: fastANI
[2023-06-30 20:56:01,571] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:56:01,572] [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_016110345.1	s__Fluviibacter phosphoraccumulans	98.7349	622	690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	99.06	98.97	0.90	0.90	3	conclusive
GCA_903870055.1	s__Fluviibacter sp903870055	83.9969	394	690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	99.89	99.89	0.98	0.98	2	-
GCA_018883265.1	s__Fluviibacter sp018883265	79.6983	238	690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883385.1	s__Fluviibacter sp018883385	79.2805	202	690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425245.1	s__Azonexus sp002425245	77.515	75	690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933675.1	s__Azonexus sp008933675	77.4433	76	690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864195.1	s__Azonexus sp016864195	77.3915	86	690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008080565.1	s__Azonexus sp008080565	77.1037	88	690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004379165.1	s__Azonexus sp004379165	77.0506	81	690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	99.94	99.94	0.95	0.95	2	-
GCF_018906035.1	s__Azo-2 sp018906035	76.1368	56	690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azo-2	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-30 20:56:01,574] [INFO] GTDB search result was written to GCA_024642425.1_ASM2464242v1_genomic.fna/result_gtdb.tsv
[2023-06-30 20:56:01,575] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:56:01,579] [INFO] DFAST_QC result json was written to GCA_024642425.1_ASM2464242v1_genomic.fna/dqc_result.json
[2023-06-30 20:56:01,579] [INFO] DFAST_QC completed!
[2023-06-30 20:56:01,579] [INFO] Total running time: 0h0m60s