[2024-01-25 18:04:20,633] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:20,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:20,634] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb4086a7-1b3e-4502-9137-6c0f09a14b7b/dqc_reference
[2024-01-25 18:04:21,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:21,786] [INFO] Task started: Prodigal
[2024-01-25 18:04:21,786] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ee61056-ebde-4050-926b-fd90ff40b7a7/GCF_016919065.1_ASM1691906v1_genomic.fna.gz | prodigal -d GCF_016919065.1_ASM1691906v1_genomic.fna/cds.fna -a GCF_016919065.1_ASM1691906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:35,811] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:35,811] [INFO] Task started: HMMsearch
[2024-01-25 18:04:35,811] [INFO] Running command: hmmsearch --tblout GCF_016919065.1_ASM1691906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb4086a7-1b3e-4502-9137-6c0f09a14b7b/dqc_reference/reference_markers.hmm GCF_016919065.1_ASM1691906v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:36,096] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:36,097] [INFO] Found 6/6 markers.
[2024-01-25 18:04:36,141] [INFO] Query marker FASTA was written to GCF_016919065.1_ASM1691906v1_genomic.fna/markers.fasta
[2024-01-25 18:04:36,141] [INFO] Task started: Blastn
[2024-01-25 18:04:36,142] [INFO] Running command: blastn -query GCF_016919065.1_ASM1691906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb4086a7-1b3e-4502-9137-6c0f09a14b7b/dqc_reference/reference_markers.fasta -out GCF_016919065.1_ASM1691906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:36,691] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:36,694] [INFO] Selected 17 target genomes.
[2024-01-25 18:04:36,694] [INFO] Target genome list was writen to GCF_016919065.1_ASM1691906v1_genomic.fna/target_genomes.txt
[2024-01-25 18:04:36,707] [INFO] Task started: fastANI
[2024-01-25 18:04:36,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ee61056-ebde-4050-926b-fd90ff40b7a7/GCF_016919065.1_ASM1691906v1_genomic.fna.gz --refList GCF_016919065.1_ASM1691906v1_genomic.fna/target_genomes.txt --output GCF_016919065.1_ASM1691906v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:49,790] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:49,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb4086a7-1b3e-4502-9137-6c0f09a14b7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:49,790] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb4086a7-1b3e-4502-9137-6c0f09a14b7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:49,798] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:04:49,798] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:49,798] [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 rhabdoformis	strain=DSM 8777	GCA_016919065.1	34032	34032	type	True	100.0	1672	1676	95	conclusive
Desulfobulbus oligotrophicus	strain=Prop6	GCA_016446285.1	1909699	1909699	type	True	79.9802	133	1676	95	below_threshold
Desulfogranum mediterraneum	strain=DSM 13871	GCA_000429965.1	160661	160661	type	True	77.1575	141	1676	95	below_threshold
Desulfobulbus elongatus	strain=DSM 2908	GCA_000621145.1	53332	53332	type	True	77.0387	198	1676	95	below_threshold
Desulfogranum japonicum	strain=DSM 18378	GCA_000429945.1	231447	231447	type	True	76.9759	96	1676	95	below_threshold
Desulfogranum marinum	strain=DSM 2058	GCA_016918565.1	453220	453220	type	True	76.801	85	1676	95	below_threshold
Desulfobulbus alkaliphilus	strain=DSM 24258	GCA_016918545.1	869814	869814	type	True	76.4692	133	1676	95	below_threshold
Desulfopila aestuarii	strain=DSM 18488	GCA_900143695.1	231440	231440	type	True	76.3999	51	1676	95	below_threshold
Desulfobulbus oralis	strain=HOT041/ORNL	GCA_002952055.1	1986146	1986146	type	True	76.327	54	1676	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:49,799] [INFO] DFAST Taxonomy check result was written to GCF_016919065.1_ASM1691906v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:49,800] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:49,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:49,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb4086a7-1b3e-4502-9137-6c0f09a14b7b/dqc_reference/checkm_data
[2024-01-25 18:04:49,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:49,855] [INFO] Task started: CheckM
[2024-01-25 18:04:49,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016919065.1_ASM1691906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016919065.1_ASM1691906v1_genomic.fna/checkm_input GCF_016919065.1_ASM1691906v1_genomic.fna/checkm_result
[2024-01-25 18:05:33,275] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:33,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:33,308] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:33,308] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:33,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016919065.1_ASM1691906v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:33,309] [INFO] Task started: Blastn
[2024-01-25 18:05:33,309] [INFO] Running command: blastn -query GCF_016919065.1_ASM1691906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb4086a7-1b3e-4502-9137-6c0f09a14b7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016919065.1_ASM1691906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:34,164] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:34,167] [INFO] Selected 20 target genomes.
[2024-01-25 18:05:34,167] [INFO] Target genome list was writen to GCF_016919065.1_ASM1691906v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:34,200] [INFO] Task started: fastANI
[2024-01-25 18:05:34,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ee61056-ebde-4050-926b-fd90ff40b7a7/GCF_016919065.1_ASM1691906v1_genomic.fna.gz --refList GCF_016919065.1_ASM1691906v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016919065.1_ASM1691906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:48,147] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:48,156] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:48,156] [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_016919065.1	s__Desulfobulbus rhabdoformis	100.0	1672	1676	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016446285.1	s__Desulfobulbus oligotrophicus	79.9682	133	1676	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429965.1	s__Desulfobulbus_A mediterraneus	77.1106	144	1676	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019163135.1	s__Desulfobulbus sp019163135	77.0462	149	1676	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429945.1	s__Desulfobulbus_A japonicus	76.9581	95	1676	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121995.1	s__Desulfobulbus sp007121995	76.8491	54	1676	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	76.8325	54	1676	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013201405.1	s__Desulfobulbus sp013201405	76.7827	61	1676	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	76.7074	145	1676	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744275.1	s__Desulfobulbus sp012744275	76.6152	66	1676	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	76.5543	92	1676	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009780825.1	s__Desulfobulbus sp009780825	76.5405	118	1676	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918545.1	s__Desulfobulbus alkaliphilus	76.4556	134	1676	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002897615.1	s__BMS3Abin13 sp002897615	76.1125	57	1676	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__BMS3Abin13	95.0	97.72	95.88	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:48,159] [INFO] GTDB search result was written to GCF_016919065.1_ASM1691906v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:48,159] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:48,165] [INFO] DFAST_QC result json was written to GCF_016919065.1_ASM1691906v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:48,165] [INFO] DFAST_QC completed!
[2024-01-25 18:05:48,165] [INFO] Total running time: 0h1m28s