[2024-01-25 20:13:50,757] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:50,759] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:50,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg571c29a7-d138-46c8-a891-7159b73a5753/dqc_reference
[2024-01-25 20:13:51,919] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:51,919] [INFO] Task started: Prodigal
[2024-01-25 20:13:51,920] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c692e53-0053-47a4-9787-681a04b9a9d3/GCF_016918545.1_ASM1691854v1_genomic.fna.gz | prodigal -d GCF_016918545.1_ASM1691854v1_genomic.fna/cds.fna -a GCF_016918545.1_ASM1691854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:02,980] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:02,980] [INFO] Task started: HMMsearch
[2024-01-25 20:14:02,981] [INFO] Running command: hmmsearch --tblout GCF_016918545.1_ASM1691854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg571c29a7-d138-46c8-a891-7159b73a5753/dqc_reference/reference_markers.hmm GCF_016918545.1_ASM1691854v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:03,275] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:03,276] [INFO] Found 6/6 markers.
[2024-01-25 20:14:03,310] [INFO] Query marker FASTA was written to GCF_016918545.1_ASM1691854v1_genomic.fna/markers.fasta
[2024-01-25 20:14:03,311] [INFO] Task started: Blastn
[2024-01-25 20:14:03,311] [INFO] Running command: blastn -query GCF_016918545.1_ASM1691854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg571c29a7-d138-46c8-a891-7159b73a5753/dqc_reference/reference_markers.fasta -out GCF_016918545.1_ASM1691854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:03,883] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:03,886] [INFO] Selected 13 target genomes.
[2024-01-25 20:14:03,886] [INFO] Target genome list was writen to GCF_016918545.1_ASM1691854v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:03,899] [INFO] Task started: fastANI
[2024-01-25 20:14:03,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c692e53-0053-47a4-9787-681a04b9a9d3/GCF_016918545.1_ASM1691854v1_genomic.fna.gz --refList GCF_016918545.1_ASM1691854v1_genomic.fna/target_genomes.txt --output GCF_016918545.1_ASM1691854v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:17,160] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:17,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg571c29a7-d138-46c8-a891-7159b73a5753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:17,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg571c29a7-d138-46c8-a891-7159b73a5753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:17,167] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:14:17,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:17,167] [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
Desulfobulbus alkaliphilus	strain=DSM 24258	GCA_016918545.1	869814	869814	type	True	100.0	1291	1293	95	conclusive
Desulfobulbus elongatus	strain=DSM 2908	GCA_000621145.1	53332	53332	type	True	77.5384	258	1293	95	below_threshold
Desulfobulbus propionicus	strain=DSM 2032	GCA_000186885.1	894	894	type	True	77.2212	282	1293	95	below_threshold
Desulfobulbus oligotrophicus	strain=Prop6	GCA_016446285.1	1909699	1909699	type	True	76.7633	99	1293	95	below_threshold
Desulfobulbus rhabdoformis	strain=DSM 8777	GCA_016919065.1	34032	34032	type	True	76.4516	127	1293	95	below_threshold
Desulfobulbus oralis	strain=HOT041/ORNL	GCA_002952055.1	1986146	1986146	type	True	76.4403	71	1293	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:17,168] [INFO] DFAST Taxonomy check result was written to GCF_016918545.1_ASM1691854v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:17,169] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:17,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:17,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg571c29a7-d138-46c8-a891-7159b73a5753/dqc_reference/checkm_data
[2024-01-25 20:14:17,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:17,214] [INFO] Task started: CheckM
[2024-01-25 20:14:17,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016918545.1_ASM1691854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016918545.1_ASM1691854v1_genomic.fna/checkm_input GCF_016918545.1_ASM1691854v1_genomic.fna/checkm_result
[2024-01-25 20:14:52,720] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:52,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.83%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:52,740] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:52,741] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:52,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016918545.1_ASM1691854v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:52,741] [INFO] Task started: Blastn
[2024-01-25 20:14:52,741] [INFO] Running command: blastn -query GCF_016918545.1_ASM1691854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg571c29a7-d138-46c8-a891-7159b73a5753/dqc_reference/reference_markers_gtdb.fasta -out GCF_016918545.1_ASM1691854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:53,520] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:53,522] [INFO] Selected 15 target genomes.
[2024-01-25 20:14:53,523] [INFO] Target genome list was writen to GCF_016918545.1_ASM1691854v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:53,535] [INFO] Task started: fastANI
[2024-01-25 20:14:53,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c692e53-0053-47a4-9787-681a04b9a9d3/GCF_016918545.1_ASM1691854v1_genomic.fna.gz --refList GCF_016918545.1_ASM1691854v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016918545.1_ASM1691854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:03,353] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:03,363] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:03,363] [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_016918545.1	s__Desulfobulbus alkaliphilus	100.0	1291	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007121995.1	s__Desulfobulbus sp007121995	84.0715	365	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621145.1	s__Desulfobulbus elongatus	77.5385	258	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842475.1	s__Desulfobulbus sp903842475	77.3833	207	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186885.1	s__Desulfobulbus propionicus	77.2307	281	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998195.1	s__Desulfobulbus sp017998195	77.2283	163	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019163135.1	s__Desulfobulbus sp019163135	77.1184	232	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009778955.1	s__Desulfobulbus sp009778955	76.9639	155	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903896915.1	s__Desulfobulbus sp903896915	76.7669	129	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015489765.1	s__DRLX01 sp015489765	76.5995	75	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003508005.1	s__UBA10518 sp003508005	76.4713	64	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__UBA10518	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151365.1	s__BMS3Abin13 sp013151365	76.4699	78	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__BMS3Abin13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919065.1	s__Desulfobulbus rhabdoformis	76.4516	127	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015493715.1	s__DRLX01 sp015493715	75.9081	56	1293	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRLX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:03,365] [INFO] GTDB search result was written to GCF_016918545.1_ASM1691854v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:03,365] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:03,368] [INFO] DFAST_QC result json was written to GCF_016918545.1_ASM1691854v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:03,368] [INFO] DFAST_QC completed!
[2024-01-25 20:15:03,368] [INFO] Total running time: 0h1m13s