[2024-01-24 13:47:10,681] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:10,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:10,683] [INFO] DQC Reference Directory: /var/lib/cwl/stgdae61b5b-cfe1-43b4-b4fa-67364ecdf960/dqc_reference
[2024-01-24 13:47:11,965] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:11,966] [INFO] Task started: Prodigal
[2024-01-24 13:47:11,966] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e651133-a012-43c2-bcb4-9f352f9fe4a4/GCF_000219915.2_ASM21991v3_genomic.fna.gz | prodigal -d GCF_000219915.2_ASM21991v3_genomic.fna/cds.fna -a GCF_000219915.2_ASM21991v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:26,221] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:26,221] [INFO] Task started: HMMsearch
[2024-01-24 13:47:26,221] [INFO] Running command: hmmsearch --tblout GCF_000219915.2_ASM21991v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdae61b5b-cfe1-43b4-b4fa-67364ecdf960/dqc_reference/reference_markers.hmm GCF_000219915.2_ASM21991v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:26,541] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:26,543] [INFO] Found 6/6 markers.
[2024-01-24 13:47:26,606] [INFO] Query marker FASTA was written to GCF_000219915.2_ASM21991v3_genomic.fna/markers.fasta
[2024-01-24 13:47:26,606] [INFO] Task started: Blastn
[2024-01-24 13:47:26,606] [INFO] Running command: blastn -query GCF_000219915.2_ASM21991v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgdae61b5b-cfe1-43b4-b4fa-67364ecdf960/dqc_reference/reference_markers.fasta -out GCF_000219915.2_ASM21991v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:27,342] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:27,347] [INFO] Selected 19 target genomes.
[2024-01-24 13:47:27,348] [INFO] Target genome list was writen to GCF_000219915.2_ASM21991v3_genomic.fna/target_genomes.txt
[2024-01-24 13:47:27,359] [INFO] Task started: fastANI
[2024-01-24 13:47:27,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e651133-a012-43c2-bcb4-9f352f9fe4a4/GCF_000219915.2_ASM21991v3_genomic.fna.gz --refList GCF_000219915.2_ASM21991v3_genomic.fna/target_genomes.txt --output GCF_000219915.2_ASM21991v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:42,684] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:42,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdae61b5b-cfe1-43b4-b4fa-67364ecdf960/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:42,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdae61b5b-cfe1-43b4-b4fa-67364ecdf960/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:42,710] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:42,710] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:42,710] [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
Advenella kashmirensis	strain=WT001	GCA_000219915.3	310575	310575	type	True	100.0	1472	1474	95	conclusive
Advenella incenata	strain=DSM 23814	GCA_004217095.1	267800	267800	type	True	90.0694	1274	1474	95	below_threshold
Advenella mimigardefordensis	strain=DPN7	GCA_000521505.1	302406	302406	type	True	84.5315	1090	1474	95	below_threshold
Advenella mandrilli	strain=WQ 585	GCA_016595155.1	2800330	2800330	type	True	77.1879	166	1474	95	below_threshold
Advenella faeciporci	strain=KCTC 23732	GCA_014652395.1	797535	797535	type	True	77.0029	176	1474	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	76.9631	147	1474	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	76.8485	111	1474	95	below_threshold
Eoetvoesia caeni	strain=DSM 25520	GCA_003315175.1	645616	645616	type	True	76.8051	113	1474	95	below_threshold
Achromobacter insolitus	strain=NCTC13520	GCA_900637265.1	217204	217204	type	True	76.6901	135	1474	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	76.6424	135	1474	95	below_threshold
Pusillimonas harenae	strain=JCM 16917	GCA_004153685.1	657015	657015	type	True	76.4901	108	1474	95	below_threshold
Pusillimonas harenae	strain=DSM 25667	GCA_013416515.1	657015	657015	type	True	76.452	107	1474	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	76.3291	148	1474	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	76.2976	153	1474	95	below_threshold
Achromobacter pestifer	strain=LMG 3431	GCA_902859625.1	1353889	1353889	type	True	76.045	148	1474	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	75.5395	76	1474	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:42,714] [INFO] DFAST Taxonomy check result was written to GCF_000219915.2_ASM21991v3_genomic.fna/tc_result.tsv
[2024-01-24 13:47:42,715] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:42,715] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:42,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdae61b5b-cfe1-43b4-b4fa-67364ecdf960/dqc_reference/checkm_data
[2024-01-24 13:47:42,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:42,761] [INFO] Task started: CheckM
[2024-01-24 13:47:42,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000219915.2_ASM21991v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000219915.2_ASM21991v3_genomic.fna/checkm_input GCF_000219915.2_ASM21991v3_genomic.fna/checkm_result
[2024-01-24 13:48:27,020] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:27,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:27,047] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:27,048] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:27,048] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000219915.2_ASM21991v3_genomic.fna/markers.fasta)
[2024-01-24 13:48:27,049] [INFO] Task started: Blastn
[2024-01-24 13:48:27,049] [INFO] Running command: blastn -query GCF_000219915.2_ASM21991v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgdae61b5b-cfe1-43b4-b4fa-67364ecdf960/dqc_reference/reference_markers_gtdb.fasta -out GCF_000219915.2_ASM21991v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:28,329] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:28,367] [INFO] Selected 6 target genomes.
[2024-01-24 13:48:28,368] [INFO] Target genome list was writen to GCF_000219915.2_ASM21991v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:28,425] [INFO] Task started: fastANI
[2024-01-24 13:48:28,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e651133-a012-43c2-bcb4-9f352f9fe4a4/GCF_000219915.2_ASM21991v3_genomic.fna.gz --refList GCF_000219915.2_ASM21991v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000219915.2_ASM21991v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:35,362] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:35,375] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:35,375] [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_000219915.2	s__Advenella kashmirensis	100.0	1472	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	98.94	98.94	0.95	0.95	2	conclusive
GCF_004217095.1	s__Advenella incenata	90.0694	1274	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	99.05	99.05	0.92	0.92	2	-
GCF_014897675.1	s__Advenella sp003533245	89.4171	1201	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	98.87	98.87	0.91	0.91	2	-
GCF_000521505.1	s__Advenella mimigardefordensis	84.5175	1090	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002810445.1	s__Advenella sp002810445	83.3967	986	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153685.1	s__Pusillimonas_C harenae	76.4901	108	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:35,377] [INFO] GTDB search result was written to GCF_000219915.2_ASM21991v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:35,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:35,381] [INFO] DFAST_QC result json was written to GCF_000219915.2_ASM21991v3_genomic.fna/dqc_result.json
[2024-01-24 13:48:35,381] [INFO] DFAST_QC completed!
[2024-01-24 13:48:35,381] [INFO] Total running time: 0h1m25s