[2024-01-24 14:14:47,487] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:47,490] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:47,490] [INFO] DQC Reference Directory: /var/lib/cwl/stg138879c5-62cd-4c47-9f28-fba6d85c8ad5/dqc_reference
[2024-01-24 14:14:49,426] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,427] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,427] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b9a5a35-0fd3-4543-b17b-f0f520f477ee/GCF_000308295.2_Ab_34632_genomic.fna.gz | prodigal -d GCF_000308295.2_Ab_34632_genomic.fna/cds.fna -a GCF_000308295.2_Ab_34632_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:06,781] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:06,781] [INFO] Task started: HMMsearch
[2024-01-24 14:15:06,781] [INFO] Running command: hmmsearch --tblout GCF_000308295.2_Ab_34632_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg138879c5-62cd-4c47-9f28-fba6d85c8ad5/dqc_reference/reference_markers.hmm GCF_000308295.2_Ab_34632_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:07,089] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:07,090] [INFO] Found 6/6 markers.
[2024-01-24 14:15:07,137] [INFO] Query marker FASTA was written to GCF_000308295.2_Ab_34632_genomic.fna/markers.fasta
[2024-01-24 14:15:07,137] [INFO] Task started: Blastn
[2024-01-24 14:15:07,137] [INFO] Running command: blastn -query GCF_000308295.2_Ab_34632_genomic.fna/markers.fasta -db /var/lib/cwl/stg138879c5-62cd-4c47-9f28-fba6d85c8ad5/dqc_reference/reference_markers.fasta -out GCF_000308295.2_Ab_34632_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:08,141] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:08,144] [INFO] Selected 15 target genomes.
[2024-01-24 14:15:08,145] [INFO] Target genome list was writen to GCF_000308295.2_Ab_34632_genomic.fna/target_genomes.txt
[2024-01-24 14:15:08,153] [INFO] Task started: fastANI
[2024-01-24 14:15:08,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b9a5a35-0fd3-4543-b17b-f0f520f477ee/GCF_000308295.2_Ab_34632_genomic.fna.gz --refList GCF_000308295.2_Ab_34632_genomic.fna/target_genomes.txt --output GCF_000308295.2_Ab_34632_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:29,769] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:29,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg138879c5-62cd-4c47-9f28-fba6d85c8ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:29,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg138879c5-62cd-4c47-9f28-fba6d85c8ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:29,785] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:29,786] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:29,786] [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
Afipia birgiae	strain=34632	GCA_000308295.2	151414	151414	type	True	99.9999	1774	1776	95	conclusive
Afipia massiliensis	strain=DSM 17498	GCA_014203115.1	211460	211460	type	True	89.4436	1308	1776	95	below_threshold
Afipia broomeae	strain=ATCC 49717	GCA_000314675.2	56946	56946	type	True	85.9436	1213	1776	95	below_threshold
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	84.1924	1148	1776	95	below_threshold
Afipia felis	strain=ATCC 53690	GCA_000314735.2	1035	1035	type	True	79.7617	583	1776	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	79.699	798	1776	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	79.6341	662	1776	95	below_threshold
Afipia carboxidovorans	strain=OM5; ATCC 49405	GCA_000021365.1	40137	40137	type	True	79.559	571	1776	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	79.5505	757	1776	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	79.4694	736	1776	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	79.4646	723	1776	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	79.4201	762	1776	95	below_threshold
Bradyrhizobium murdochi	strain=WSM 1741	GCA_000472965.1	1038859	1038859	type	True	79.274	738	1776	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	79.1184	728	1776	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	79.026	697	1776	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:29,787] [INFO] DFAST Taxonomy check result was written to GCF_000308295.2_Ab_34632_genomic.fna/tc_result.tsv
[2024-01-24 14:15:29,788] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:29,788] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:29,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg138879c5-62cd-4c47-9f28-fba6d85c8ad5/dqc_reference/checkm_data
[2024-01-24 14:15:29,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:29,841] [INFO] Task started: CheckM
[2024-01-24 14:15:29,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000308295.2_Ab_34632_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000308295.2_Ab_34632_genomic.fna/checkm_input GCF_000308295.2_Ab_34632_genomic.fna/checkm_result
[2024-01-24 14:16:17,309] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:17,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:17,329] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:17,330] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:17,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000308295.2_Ab_34632_genomic.fna/markers.fasta)
[2024-01-24 14:16:17,330] [INFO] Task started: Blastn
[2024-01-24 14:16:17,331] [INFO] Running command: blastn -query GCF_000308295.2_Ab_34632_genomic.fna/markers.fasta -db /var/lib/cwl/stg138879c5-62cd-4c47-9f28-fba6d85c8ad5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000308295.2_Ab_34632_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:19,202] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:19,206] [INFO] Selected 8 target genomes.
[2024-01-24 14:16:19,206] [INFO] Target genome list was writen to GCF_000308295.2_Ab_34632_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:19,216] [INFO] Task started: fastANI
[2024-01-24 14:16:19,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b9a5a35-0fd3-4543-b17b-f0f520f477ee/GCF_000308295.2_Ab_34632_genomic.fna.gz --refList GCF_000308295.2_Ab_34632_genomic.fna/target_genomes_gtdb.txt --output GCF_000308295.2_Ab_34632_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:29,101] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:29,116] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:29,116] [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_000308295.2	s__Afipia birgiae	99.9999	1774	1776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	98.96	98.31	0.86	0.83	3	conclusive
GCF_014203115.1	s__Afipia massiliensis	89.443	1308	1776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001006325.2	s__Afipia massiliensis_A	89.4194	1225	1776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017474385.1	s__Afipia sp017474385	86.4577	969	1776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314675.2	s__Afipia broomeae	85.9575	1210	1776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	97.99	97.77	0.89	0.84	9	-
GCF_000497575.1	s__Afipia sp000497575	85.7822	1159	1776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.26	97.37	0.94	0.78	8	-
GCF_000336555.1	s__Afipia clevelandensis	84.1924	1148	1776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	97.84	97.84	0.91	0.91	2	-
GCA_017308495.1	s__Afipia sp017308495	81.941	782	1776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:29,118] [INFO] GTDB search result was written to GCF_000308295.2_Ab_34632_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:29,119] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:29,122] [INFO] DFAST_QC result json was written to GCF_000308295.2_Ab_34632_genomic.fna/dqc_result.json
[2024-01-24 14:16:29,122] [INFO] DFAST_QC completed!
[2024-01-24 14:16:29,122] [INFO] Total running time: 0h1m42s