[2023-06-27 05:39:09,439] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:39:09,441] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:39:09,441] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d802ccd-a117-4ad5-9511-dc412ba292f6/dqc_reference
[2023-06-27 05:39:10,749] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:39:10,751] [INFO] Task started: Prodigal
[2023-06-27 05:39:10,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg215287c9-d64c-45a0-8bc2-988887655c68/GCA_026003855.1_ASM2600385v1_genomic.fna.gz | prodigal -d GCA_026003855.1_ASM2600385v1_genomic.fna/cds.fna -a GCA_026003855.1_ASM2600385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:39:30,785] [INFO] Task succeeded: Prodigal
[2023-06-27 05:39:30,786] [INFO] Task started: HMMsearch
[2023-06-27 05:39:30,786] [INFO] Running command: hmmsearch --tblout GCA_026003855.1_ASM2600385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d802ccd-a117-4ad5-9511-dc412ba292f6/dqc_reference/reference_markers.hmm GCA_026003855.1_ASM2600385v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:39:31,126] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:39:31,128] [INFO] Found 6/6 markers.
[2023-06-27 05:39:31,187] [INFO] Query marker FASTA was written to GCA_026003855.1_ASM2600385v1_genomic.fna/markers.fasta
[2023-06-27 05:39:31,187] [INFO] Task started: Blastn
[2023-06-27 05:39:31,187] [INFO] Running command: blastn -query GCA_026003855.1_ASM2600385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d802ccd-a117-4ad5-9511-dc412ba292f6/dqc_reference/reference_markers.fasta -out GCA_026003855.1_ASM2600385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:39:31,819] [INFO] Task succeeded: Blastn
[2023-06-27 05:39:31,823] [INFO] Selected 15 target genomes.
[2023-06-27 05:39:31,823] [INFO] Target genome list was writen to GCA_026003855.1_ASM2600385v1_genomic.fna/target_genomes.txt
[2023-06-27 05:39:31,827] [INFO] Task started: fastANI
[2023-06-27 05:39:31,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg215287c9-d64c-45a0-8bc2-988887655c68/GCA_026003855.1_ASM2600385v1_genomic.fna.gz --refList GCA_026003855.1_ASM2600385v1_genomic.fna/target_genomes.txt --output GCA_026003855.1_ASM2600385v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:39:51,473] [INFO] Task succeeded: fastANI
[2023-06-27 05:39:51,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d802ccd-a117-4ad5-9511-dc412ba292f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:39:51,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d802ccd-a117-4ad5-9511-dc412ba292f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:39:51,482] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-27 05:39:51,482] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 05:39:51,482] [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
Roseiflexus castenholzii	strain=DSM 13941	GCA_000017805.1	120962	120962	type	True	98.4388	1783	1857	95	conclusive
Chloroflexus aggregans	strain=DSM 9485	GCA_000021945.1	152260	152260	type	True	82.3516	111	1857	95	below_threshold
Chloroflexus islandicus	strain=isl-2	GCA_001650695.1	1707952	1707952	type	True	75.9358	130	1857	95	below_threshold
Chloroflexus aurantiacus	strain=J-10-fl	GCA_000018865.1	1108	1108	type	True	75.869	90	1857	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	74.9549	56	1857	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	74.7641	67	1857	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:39:51,484] [INFO] DFAST Taxonomy check result was written to GCA_026003855.1_ASM2600385v1_genomic.fna/tc_result.tsv
[2023-06-27 05:39:51,485] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:39:51,485] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:39:51,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d802ccd-a117-4ad5-9511-dc412ba292f6/dqc_reference/checkm_data
[2023-06-27 05:39:51,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:39:51,541] [INFO] Task started: CheckM
[2023-06-27 05:39:51,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026003855.1_ASM2600385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026003855.1_ASM2600385v1_genomic.fna/checkm_input GCA_026003855.1_ASM2600385v1_genomic.fna/checkm_result
[2023-06-27 05:40:52,940] [INFO] Task succeeded: CheckM
[2023-06-27 05:40:52,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:40:52,969] [INFO] ===== Completeness check finished =====
[2023-06-27 05:40:52,969] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:40:52,969] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026003855.1_ASM2600385v1_genomic.fna/markers.fasta)
[2023-06-27 05:40:52,970] [INFO] Task started: Blastn
[2023-06-27 05:40:52,970] [INFO] Running command: blastn -query GCA_026003855.1_ASM2600385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d802ccd-a117-4ad5-9511-dc412ba292f6/dqc_reference/reference_markers_gtdb.fasta -out GCA_026003855.1_ASM2600385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:40:53,791] [INFO] Task succeeded: Blastn
[2023-06-27 05:40:53,795] [INFO] Selected 12 target genomes.
[2023-06-27 05:40:53,796] [INFO] Target genome list was writen to GCA_026003855.1_ASM2600385v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:40:53,803] [INFO] Task started: fastANI
[2023-06-27 05:40:53,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg215287c9-d64c-45a0-8bc2-988887655c68/GCA_026003855.1_ASM2600385v1_genomic.fna.gz --refList GCA_026003855.1_ASM2600385v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026003855.1_ASM2600385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:41:12,330] [INFO] Task succeeded: fastANI
[2023-06-27 05:41:12,340] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:41:12,340] [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_000017805.1	s__Roseiflexus castenholzii	98.4345	1783	1857	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Roseiflexus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000016665.1	s__Roseiflexus sp000016665	80.0564	1196	1857	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Roseiflexus	95.0	98.43	98.43	0.97	0.97	2	-
GCA_017743475.1	s__Roseiflexus sp017743475	78.8662	897	1857	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Roseiflexus	95.0	98.84	95.62	0.92	0.85	6	-
GCA_013388755.1	s__JACAEQ01 sp013388755	77.0846	454	1857	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__JACAEQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001399705.1	s__Kouleothrix aurantiaca	76.2363	62	1857	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Kouleothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266315.1	s__Kouleothrix sp018266315	75.9994	74	1857	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Kouleothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717335.1	s__JADKFS01 sp016717335	75.9551	221	1857	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__JADKFS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016722075.1	s__Kouleothrix sp016722075	75.9458	163	1857	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Kouleothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012031775.1	s__JAAUTF01 sp012031775	75.6119	71	1857	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__JAAUTF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138165.1	s__Chloroploca sp004138165	75.3072	68	1857	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Chloroploca	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 05:41:12,342] [INFO] GTDB search result was written to GCA_026003855.1_ASM2600385v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:41:12,343] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:41:12,349] [INFO] DFAST_QC result json was written to GCA_026003855.1_ASM2600385v1_genomic.fna/dqc_result.json
[2023-06-27 05:41:12,350] [INFO] DFAST_QC completed!
[2023-06-27 05:41:12,350] [INFO] Total running time: 0h2m3s