[2024-01-24 14:38:49,868] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:49,870] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:49,870] [INFO] DQC Reference Directory: /var/lib/cwl/stg19c1549e-ba3d-4ab8-8766-29a2cf68d869/dqc_reference
[2024-01-24 14:38:52,371] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:52,372] [INFO] Task started: Prodigal
[2024-01-24 14:38:52,373] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ab4beaf-34fb-4586-8992-853ed25a3056/GCF_005871185.1_ASM587118v1_genomic.fna.gz | prodigal -d GCF_005871185.1_ASM587118v1_genomic.fna/cds.fna -a GCF_005871185.1_ASM587118v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:05,551] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:05,552] [INFO] Task started: HMMsearch
[2024-01-24 14:39:05,552] [INFO] Running command: hmmsearch --tblout GCF_005871185.1_ASM587118v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19c1549e-ba3d-4ab8-8766-29a2cf68d869/dqc_reference/reference_markers.hmm GCF_005871185.1_ASM587118v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:05,866] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:05,867] [INFO] Found 6/6 markers.
[2024-01-24 14:39:05,904] [INFO] Query marker FASTA was written to GCF_005871185.1_ASM587118v1_genomic.fna/markers.fasta
[2024-01-24 14:39:05,905] [INFO] Task started: Blastn
[2024-01-24 14:39:05,905] [INFO] Running command: blastn -query GCF_005871185.1_ASM587118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19c1549e-ba3d-4ab8-8766-29a2cf68d869/dqc_reference/reference_markers.fasta -out GCF_005871185.1_ASM587118v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:06,706] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:06,709] [INFO] Selected 25 target genomes.
[2024-01-24 14:39:06,709] [INFO] Target genome list was writen to GCF_005871185.1_ASM587118v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:06,725] [INFO] Task started: fastANI
[2024-01-24 14:39:06,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ab4beaf-34fb-4586-8992-853ed25a3056/GCF_005871185.1_ASM587118v1_genomic.fna.gz --refList GCF_005871185.1_ASM587118v1_genomic.fna/target_genomes.txt --output GCF_005871185.1_ASM587118v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:23,970] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:23,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19c1549e-ba3d-4ab8-8766-29a2cf68d869/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:23,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19c1549e-ba3d-4ab8-8766-29a2cf68d869/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:23,978] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:23,978] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:23,979] [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
Limnobacter alexandrii	strain=LZ-4	GCA_005871185.1	2570352	2570352	type	True	100.0	1155	1155	95	conclusive
Limnobacter humi	strain=NBRC 111650	GCA_024518835.1	1778671	1778671	type	True	78.6476	377	1155	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	76.2712	55	1155	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	76.1484	52	1155	95	below_threshold
Achromobacter piechaudii	strain=LMG 1873	GCA_902859685.1	72556	72556	type	True	75.9634	51	1155	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	75.6779	54	1155	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:23,980] [INFO] DFAST Taxonomy check result was written to GCF_005871185.1_ASM587118v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:23,981] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:23,981] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:23,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19c1549e-ba3d-4ab8-8766-29a2cf68d869/dqc_reference/checkm_data
[2024-01-24 14:39:23,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:24,025] [INFO] Task started: CheckM
[2024-01-24 14:39:24,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005871185.1_ASM587118v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005871185.1_ASM587118v1_genomic.fna/checkm_input GCF_005871185.1_ASM587118v1_genomic.fna/checkm_result
[2024-01-24 14:40:06,810] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:06,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:06,833] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:06,833] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:06,833] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005871185.1_ASM587118v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:06,834] [INFO] Task started: Blastn
[2024-01-24 14:40:06,834] [INFO] Running command: blastn -query GCF_005871185.1_ASM587118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19c1549e-ba3d-4ab8-8766-29a2cf68d869/dqc_reference/reference_markers_gtdb.fasta -out GCF_005871185.1_ASM587118v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:08,084] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:08,088] [INFO] Selected 9 target genomes.
[2024-01-24 14:40:08,089] [INFO] Target genome list was writen to GCF_005871185.1_ASM587118v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:08,098] [INFO] Task started: fastANI
[2024-01-24 14:40:08,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ab4beaf-34fb-4586-8992-853ed25a3056/GCF_005871185.1_ASM587118v1_genomic.fna.gz --refList GCF_005871185.1_ASM587118v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005871185.1_ASM587118v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:16,294] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:16,308] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:16,309] [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_005871185.1	s__Limnobacter alexandrii	100.0	1155	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_902506325.1	s__Limnobacter sp902506325	86.745	942	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004065.1	s__Limnobacter sp002954425	86.274	926	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	97.67	96.02	0.92	0.87	19	-
GCF_000170915.1	s__Limnobacter sp000170915	86.0841	887	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	98.10	98.01	0.88	0.86	5	-
GCA_001601825.1	s__Limnobacter sp001601825	85.2312	852	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018812945.1	s__Limnobacter sp018812945	85.2162	761	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018815245.1	s__Limnobacter sp018815245	83.0073	767	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	99.98	99.93	0.99	0.98	9	-
GCA_004291335.1	s__Limnobacter thiooxidans	81.3936	676	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:16,311] [INFO] GTDB search result was written to GCF_005871185.1_ASM587118v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:16,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:16,315] [INFO] DFAST_QC result json was written to GCF_005871185.1_ASM587118v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:16,315] [INFO] DFAST_QC completed!
[2024-01-24 14:40:16,315] [INFO] Total running time: 0h1m26s