[2023-06-27 21:27:27,066] [INFO] DFAST_QC pipeline started.
[2023-06-27 21:27:27,081] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 21:27:27,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg484c9bc2-897e-47f9-be9e-00f82da71639/dqc_reference
[2023-06-27 21:27:28,654] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 21:27:28,655] [INFO] Task started: Prodigal
[2023-06-27 21:27:28,655] [INFO] Running command: gunzip -c /var/lib/cwl/stga534902e-b5e3-43b9-b19d-b014a7408eda/GCA_026995045.1_ASM2699504v1_genomic.fna.gz | prodigal -d GCA_026995045.1_ASM2699504v1_genomic.fna/cds.fna -a GCA_026995045.1_ASM2699504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 21:27:39,047] [INFO] Task succeeded: Prodigal
[2023-06-27 21:27:39,047] [INFO] Task started: HMMsearch
[2023-06-27 21:27:39,048] [INFO] Running command: hmmsearch --tblout GCA_026995045.1_ASM2699504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg484c9bc2-897e-47f9-be9e-00f82da71639/dqc_reference/reference_markers.hmm GCA_026995045.1_ASM2699504v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 21:27:39,339] [INFO] Task succeeded: HMMsearch
[2023-06-27 21:27:39,341] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga534902e-b5e3-43b9-b19d-b014a7408eda/GCA_026995045.1_ASM2699504v1_genomic.fna.gz]
[2023-06-27 21:27:39,373] [INFO] Query marker FASTA was written to GCA_026995045.1_ASM2699504v1_genomic.fna/markers.fasta
[2023-06-27 21:27:39,373] [INFO] Task started: Blastn
[2023-06-27 21:27:39,374] [INFO] Running command: blastn -query GCA_026995045.1_ASM2699504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg484c9bc2-897e-47f9-be9e-00f82da71639/dqc_reference/reference_markers.fasta -out GCA_026995045.1_ASM2699504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 21:27:40,183] [INFO] Task succeeded: Blastn
[2023-06-27 21:27:40,188] [INFO] Selected 21 target genomes.
[2023-06-27 21:27:40,189] [INFO] Target genome list was writen to GCA_026995045.1_ASM2699504v1_genomic.fna/target_genomes.txt
[2023-06-27 21:27:40,191] [INFO] Task started: fastANI
[2023-06-27 21:27:40,191] [INFO] Running command: fastANI --query /var/lib/cwl/stga534902e-b5e3-43b9-b19d-b014a7408eda/GCA_026995045.1_ASM2699504v1_genomic.fna.gz --refList GCA_026995045.1_ASM2699504v1_genomic.fna/target_genomes.txt --output GCA_026995045.1_ASM2699504v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 21:27:53,276] [INFO] Task succeeded: fastANI
[2023-06-27 21:27:53,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg484c9bc2-897e-47f9-be9e-00f82da71639/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 21:27:53,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg484c9bc2-897e-47f9-be9e-00f82da71639/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 21:27:53,292] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 21:27:53,292] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 21:27:53,292] [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
Thiogranum longum	strain=DSM 19610	GCA_004339085.1	1537524	1537524	type	True	76.7852	59	950	95	below_threshold
Acidihalobacter prosperus	strain=DSM 5130	GCA_000754095.2	160660	160660	type	True	76.7788	50	950	95	below_threshold
Sulfuricaulis limicola	strain=HA5	GCA_002355735.1	1620215	1620215	type	True	76.4928	71	950	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.4291	69	950	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.4183	82	950	95	below_threshold
Thiohalophilus thiocyanatoxydans	strain=DSM 16326	GCA_004366735.1	381308	381308	type	True	76.3964	67	950	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.1801	68	950	95	below_threshold
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	76.0397	79	950	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	76.0233	60	950	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	75.9383	63	950	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	75.7572	67	950	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 21:27:53,296] [INFO] DFAST Taxonomy check result was written to GCA_026995045.1_ASM2699504v1_genomic.fna/tc_result.tsv
[2023-06-27 21:27:53,296] [INFO] ===== Taxonomy check completed =====
[2023-06-27 21:27:53,297] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 21:27:53,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg484c9bc2-897e-47f9-be9e-00f82da71639/dqc_reference/checkm_data
[2023-06-27 21:27:53,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 21:27:53,336] [INFO] Task started: CheckM
[2023-06-27 21:27:53,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026995045.1_ASM2699504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026995045.1_ASM2699504v1_genomic.fna/checkm_input GCA_026995045.1_ASM2699504v1_genomic.fna/checkm_result
[2023-06-27 21:28:28,439] [INFO] Task succeeded: CheckM
[2023-06-27 21:28:28,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.64%
Contamintation: 5.73%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-27 21:28:28,462] [INFO] ===== Completeness check finished =====
[2023-06-27 21:28:28,463] [INFO] ===== Start GTDB Search =====
[2023-06-27 21:28:28,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026995045.1_ASM2699504v1_genomic.fna/markers.fasta)
[2023-06-27 21:28:28,464] [INFO] Task started: Blastn
[2023-06-27 21:28:28,464] [INFO] Running command: blastn -query GCA_026995045.1_ASM2699504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg484c9bc2-897e-47f9-be9e-00f82da71639/dqc_reference/reference_markers_gtdb.fasta -out GCA_026995045.1_ASM2699504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 21:28:29,840] [INFO] Task succeeded: Blastn
[2023-06-27 21:28:29,845] [INFO] Selected 21 target genomes.
[2023-06-27 21:28:29,845] [INFO] Target genome list was writen to GCA_026995045.1_ASM2699504v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 21:28:29,854] [INFO] Task started: fastANI
[2023-06-27 21:28:29,854] [INFO] Running command: fastANI --query /var/lib/cwl/stga534902e-b5e3-43b9-b19d-b014a7408eda/GCA_026995045.1_ASM2699504v1_genomic.fna.gz --refList GCA_026995045.1_ASM2699504v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026995045.1_ASM2699504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 21:28:40,787] [INFO] Task succeeded: fastANI
[2023-06-27 21:28:40,806] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 21:28:40,807] [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
GCA_011051475.1	s__GCA-2746365 sp011051475	77.6675	150	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-229;f__SZUA-229;g__GCA-2746365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494295.1	s__Thiogranum sp015494295	77.2977	126	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	99.47	99.47	0.86	0.86	2	-
GCA_015488295.1	s__GCA-2746365 sp015488295	77.0959	144	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-229;f__SZUA-229;g__GCA-2746365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	76.9521	74	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	76.9459	111	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCF_004339085.1	s__Thiogranum longum	76.7869	58	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000754095.2	s__Acidihalobacter prosperus	76.7788	50	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Acidihalobacteraceae;g__Acidihalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015484935.1	s__S139-92 sp015484935	76.7742	85	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-229;f__SZUA-229;g__S139-92	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005240065.1	s__Ga0077554 sp005240065	76.6513	63	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077554;f__Ga007554;g__Ga0077554	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008632335.1	s__Thiohalocapsa marina	76.4183	82	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015484945.1	s__WFUO01 sp015484945	76.3364	63	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__WFUO01;f__WFUO01;g__WFUO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389885.1	s__JABBTK01 sp011389885	76.1806	63	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__JABBTK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107375.1	s__Lysobacter sp900107375	75.9832	72	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007695245.1	s__REEE01 sp007695245	75.9678	67	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__REEE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013178375.1	s__Ch67 sp013178375	75.964	68	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ch67	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485125.1	s__S139-57 sp015485125	75.9173	60	950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__S139-57;g__S139-57	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 21:28:40,809] [INFO] GTDB search result was written to GCA_026995045.1_ASM2699504v1_genomic.fna/result_gtdb.tsv
[2023-06-27 21:28:40,810] [INFO] ===== GTDB Search completed =====
[2023-06-27 21:28:40,816] [INFO] DFAST_QC result json was written to GCA_026995045.1_ASM2699504v1_genomic.fna/dqc_result.json
[2023-06-27 21:28:40,817] [INFO] DFAST_QC completed!
[2023-06-27 21:28:40,817] [INFO] Total running time: 0h1m14s