[2024-01-25 20:17:50,348] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:50,351] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:50,351] [INFO] DQC Reference Directory: /var/lib/cwl/stgcae477a5-d1a1-4fbe-994a-c29938911f06/dqc_reference
[2024-01-25 20:17:51,474] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:51,475] [INFO] Task started: Prodigal
[2024-01-25 20:17:51,475] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7cd9f75-dfc1-4c0e-b490-4ace1144416c/GCF_014199525.1_ASM1419952v1_genomic.fna.gz | prodigal -d GCF_014199525.1_ASM1419952v1_genomic.fna/cds.fna -a GCF_014199525.1_ASM1419952v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:01,810] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:01,810] [INFO] Task started: HMMsearch
[2024-01-25 20:18:01,810] [INFO] Running command: hmmsearch --tblout GCF_014199525.1_ASM1419952v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcae477a5-d1a1-4fbe-994a-c29938911f06/dqc_reference/reference_markers.hmm GCF_014199525.1_ASM1419952v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:02,039] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:02,040] [INFO] Found 6/6 markers.
[2024-01-25 20:18:02,082] [INFO] Query marker FASTA was written to GCF_014199525.1_ASM1419952v1_genomic.fna/markers.fasta
[2024-01-25 20:18:02,082] [INFO] Task started: Blastn
[2024-01-25 20:18:02,082] [INFO] Running command: blastn -query GCF_014199525.1_ASM1419952v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcae477a5-d1a1-4fbe-994a-c29938911f06/dqc_reference/reference_markers.fasta -out GCF_014199525.1_ASM1419952v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:02,770] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:02,774] [INFO] Selected 9 target genomes.
[2024-01-25 20:18:02,774] [INFO] Target genome list was writen to GCF_014199525.1_ASM1419952v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:02,780] [INFO] Task started: fastANI
[2024-01-25 20:18:02,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7cd9f75-dfc1-4c0e-b490-4ace1144416c/GCF_014199525.1_ASM1419952v1_genomic.fna.gz --refList GCF_014199525.1_ASM1419952v1_genomic.fna/target_genomes.txt --output GCF_014199525.1_ASM1419952v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:17,753] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:17,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcae477a5-d1a1-4fbe-994a-c29938911f06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:17,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcae477a5-d1a1-4fbe-994a-c29938911f06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:17,760] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:18:17,760] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:17,761] [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
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	100.0	1725	1725	95	conclusive
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	84.5539	1175	1725	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	77.8599	784	1725	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	77.8223	725	1725	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	77.6818	692	1725	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	77.6476	726	1725	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	77.3219	822	1725	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	76.9501	625	1725	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	75.1498	349	1725	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:17,762] [INFO] DFAST Taxonomy check result was written to GCF_014199525.1_ASM1419952v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:17,763] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:17,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:17,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcae477a5-d1a1-4fbe-994a-c29938911f06/dqc_reference/checkm_data
[2024-01-25 20:18:17,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:17,812] [INFO] Task started: CheckM
[2024-01-25 20:18:17,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199525.1_ASM1419952v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199525.1_ASM1419952v1_genomic.fna/checkm_input GCF_014199525.1_ASM1419952v1_genomic.fna/checkm_result
[2024-01-25 20:19:04,828] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:04,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:04,844] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:04,845] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:04,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199525.1_ASM1419952v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:04,845] [INFO] Task started: Blastn
[2024-01-25 20:19:04,845] [INFO] Running command: blastn -query GCF_014199525.1_ASM1419952v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcae477a5-d1a1-4fbe-994a-c29938911f06/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199525.1_ASM1419952v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:06,050] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:06,052] [INFO] Selected 12 target genomes.
[2024-01-25 20:19:06,053] [INFO] Target genome list was writen to GCF_014199525.1_ASM1419952v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:06,074] [INFO] Task started: fastANI
[2024-01-25 20:19:06,075] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7cd9f75-dfc1-4c0e-b490-4ace1144416c/GCF_014199525.1_ASM1419952v1_genomic.fna.gz --refList GCF_014199525.1_ASM1419952v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199525.1_ASM1419952v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:23,090] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:23,098] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:23,098] [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_014199525.1	s__Conexibacter arvalis	100.0	1725	1725	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000025265.1	s__Conexibacter woesei	84.4298	1190	1725	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268595.1	s__Conexibacter sp018268595	81.661	787	1725	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655225.1	s__Conexibacter sp015655225	80.3257	579	1725	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815355.1	s__Palsa-744 sp013815355	78.2697	358	1725	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215085.1	s__Baekduia sp016215085	77.9278	565	1725	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003044185.1	s__SEOHO-28 sp003044185	77.7994	729	1725	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	98.17	98.17	0.92	0.92	2	-
GCA_902806175.1	s__CADCVQ01 sp902806175	77.7787	600	1725	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695395.1	s__SEOHO-28 sp013695395	77.7453	348	1725	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240115.1	s__Palsa-465 sp019240115	77.7133	595	1725	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000688095.1	s__Baekduia sp000688095	77.6421	853	1725	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970665.1	s__Baekduia soli	77.5674	746	1725	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:23,101] [INFO] GTDB search result was written to GCF_014199525.1_ASM1419952v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:23,102] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:23,105] [INFO] DFAST_QC result json was written to GCF_014199525.1_ASM1419952v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:23,105] [INFO] DFAST_QC completed!
[2024-01-25 20:19:23,105] [INFO] Total running time: 0h1m33s