[2024-01-24 13:19:13,114] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:13,117] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:13,117] [INFO] DQC Reference Directory: /var/lib/cwl/stg6696b8f7-fcbe-4dcd-a758-8a502801758d/dqc_reference
[2024-01-24 13:19:14,393] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:14,394] [INFO] Task started: Prodigal
[2024-01-24 13:19:14,395] [INFO] Running command: gunzip -c /var/lib/cwl/stgeaf6581e-6d8b-42cb-92b8-b12ac617f931/GCF_013283665.1_ASM1328366v1_genomic.fna.gz | prodigal -d GCF_013283665.1_ASM1328366v1_genomic.fna/cds.fna -a GCF_013283665.1_ASM1328366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:34,814] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:34,815] [INFO] Task started: HMMsearch
[2024-01-24 13:19:34,815] [INFO] Running command: hmmsearch --tblout GCF_013283665.1_ASM1328366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6696b8f7-fcbe-4dcd-a758-8a502801758d/dqc_reference/reference_markers.hmm GCF_013283665.1_ASM1328366v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:35,137] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:35,139] [INFO] Found 6/6 markers.
[2024-01-24 13:19:35,208] [INFO] Query marker FASTA was written to GCF_013283665.1_ASM1328366v1_genomic.fna/markers.fasta
[2024-01-24 13:19:35,208] [INFO] Task started: Blastn
[2024-01-24 13:19:35,208] [INFO] Running command: blastn -query GCF_013283665.1_ASM1328366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6696b8f7-fcbe-4dcd-a758-8a502801758d/dqc_reference/reference_markers.fasta -out GCF_013283665.1_ASM1328366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:36,262] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:36,266] [INFO] Selected 21 target genomes.
[2024-01-24 13:19:36,266] [INFO] Target genome list was writen to GCF_013283665.1_ASM1328366v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:36,280] [INFO] Task started: fastANI
[2024-01-24 13:19:36,280] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaf6581e-6d8b-42cb-92b8-b12ac617f931/GCF_013283665.1_ASM1328366v1_genomic.fna.gz --refList GCF_013283665.1_ASM1328366v1_genomic.fna/target_genomes.txt --output GCF_013283665.1_ASM1328366v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:03,275] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:03,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6696b8f7-fcbe-4dcd-a758-8a502801758d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:03,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6696b8f7-fcbe-4dcd-a758-8a502801758d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:03,295] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:20:03,295] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:20:03,295] [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
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	100.0	2296	2297	95	conclusive
Sinorhizobium fredii	strain=USDA205	GCA_009601405.1	380	380	type	True	82.248	1205	2297	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	82.2208	1174	2297	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	82.2132	1154	2297	95	below_threshold
Ensifer psoraleae	strain=CCBAU 65732	GCA_013283645.1	520838	520838	type	True	82.1964	1291	2297	95	below_threshold
Ensifer mexicanus	strain=ITTG R7	GCA_013488225.1	375549	375549	type	True	81.8896	1176	2297	95	below_threshold
Ensifer mexicanus	strain=DSM 18446	GCA_017873105.1	375549	375549	type	True	81.8838	1169	2297	95	below_threshold
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	81.6978	1052	2297	95	below_threshold
Sinorhizobium meliloti	strain=USDA1002	GCA_009601385.1	382	382	type	True	81.5974	1088	2297	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	81.3421	1014	2297	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	81.3143	843	2297	95	below_threshold
Sinorhizobium kostiense	strain=DSM 13372	GCA_017874595.1	76747	76747	type	True	81.2723	1041	2297	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	81.2698	1014	2297	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	81.2207	841	2297	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	81.2122	855	2297	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	80.9432	875	2297	95	below_threshold
Rhizobium giardinii	strain=H152	GCA_000379605.1	56731	56731	type	True	80.7733	972	2297	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	79.9233	812	2297	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	79.8944	840	2297	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	79.8854	841	2297	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.6925	680	2297	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:03,297] [INFO] DFAST Taxonomy check result was written to GCF_013283665.1_ASM1328366v1_genomic.fna/tc_result.tsv
[2024-01-24 13:20:03,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:03,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:03,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6696b8f7-fcbe-4dcd-a758-8a502801758d/dqc_reference/checkm_data
[2024-01-24 13:20:03,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:03,367] [INFO] Task started: CheckM
[2024-01-24 13:20:03,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013283665.1_ASM1328366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013283665.1_ASM1328366v1_genomic.fna/checkm_input GCF_013283665.1_ASM1328366v1_genomic.fna/checkm_result
[2024-01-24 13:21:01,056] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:01,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:01,081] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:01,081] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:01,081] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013283665.1_ASM1328366v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:01,082] [INFO] Task started: Blastn
[2024-01-24 13:21:01,082] [INFO] Running command: blastn -query GCF_013283665.1_ASM1328366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6696b8f7-fcbe-4dcd-a758-8a502801758d/dqc_reference/reference_markers_gtdb.fasta -out GCF_013283665.1_ASM1328366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:03,217] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:03,220] [INFO] Selected 8 target genomes.
[2024-01-24 13:21:03,220] [INFO] Target genome list was writen to GCF_013283665.1_ASM1328366v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:03,233] [INFO] Task started: fastANI
[2024-01-24 13:21:03,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaf6581e-6d8b-42cb-92b8-b12ac617f931/GCF_013283665.1_ASM1328366v1_genomic.fna.gz --refList GCF_013283665.1_ASM1328366v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013283665.1_ASM1328366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:17,121] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:17,133] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:17,133] [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_013283665.1	s__Ensifer sesbaniae	100.0	2296	2297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.93	98.93	0.89	0.89	2	conclusive
GCF_001429285.1	s__Ensifer sp001429285	89.7657	1789	2297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	97.69	95.18	0.90	0.85	16	-
GCA_900469595.1	s__Ensifer sp900469595	88.6849	1710	2297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.13	98.13	0.88	0.88	2	-
GCF_002007205.1	s__Ensifer adhaerens_D	87.5168	1632	2297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002940685.1	s__Ensifer adhaerens_E	87.3925	1670	2297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001695835.1	s__Ensifer sp001695835	87.38	1583	2297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	100.00	100.00	1.00	0.99	4	-
GCF_016919405.1	s__Ensifer sp000799055	87.271	1599	2297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	97.37	96.05	0.91	0.88	3	-
GCF_000697965.2	s__Ensifer adhaerens	87.2111	1674	2297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.67	95.82	0.92	0.87	37	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:17,140] [INFO] GTDB search result was written to GCF_013283665.1_ASM1328366v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:17,141] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:17,152] [INFO] DFAST_QC result json was written to GCF_013283665.1_ASM1328366v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:17,152] [INFO] DFAST_QC completed!
[2024-01-24 13:21:17,153] [INFO] Total running time: 0h2m4s