[2024-01-24 15:18:34,660] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:34,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:34,662] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d35160b-0547-4802-92ac-9e1efdc8c804/dqc_reference
[2024-01-24 15:18:38,356] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:38,358] [INFO] Task started: Prodigal
[2024-01-24 15:18:38,358] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b248ca3-1719-4d0b-b554-093db2d01f55/GCF_013128195.2_ASM1312819v2_genomic.fna.gz | prodigal -d GCF_013128195.2_ASM1312819v2_genomic.fna/cds.fna -a GCF_013128195.2_ASM1312819v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:08,162] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:08,163] [INFO] Task started: HMMsearch
[2024-01-24 15:19:08,163] [INFO] Running command: hmmsearch --tblout GCF_013128195.2_ASM1312819v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d35160b-0547-4802-92ac-9e1efdc8c804/dqc_reference/reference_markers.hmm GCF_013128195.2_ASM1312819v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:08,597] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:08,598] [INFO] Found 6/6 markers.
[2024-01-24 15:19:08,690] [INFO] Query marker FASTA was written to GCF_013128195.2_ASM1312819v2_genomic.fna/markers.fasta
[2024-01-24 15:19:08,691] [INFO] Task started: Blastn
[2024-01-24 15:19:08,691] [INFO] Running command: blastn -query GCF_013128195.2_ASM1312819v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d35160b-0547-4802-92ac-9e1efdc8c804/dqc_reference/reference_markers.fasta -out GCF_013128195.2_ASM1312819v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:09,357] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:09,361] [INFO] Selected 11 target genomes.
[2024-01-24 15:19:09,361] [INFO] Target genome list was writen to GCF_013128195.2_ASM1312819v2_genomic.fna/target_genomes.txt
[2024-01-24 15:19:09,366] [INFO] Task started: fastANI
[2024-01-24 15:19:09,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b248ca3-1719-4d0b-b554-093db2d01f55/GCF_013128195.2_ASM1312819v2_genomic.fna.gz --refList GCF_013128195.2_ASM1312819v2_genomic.fna/target_genomes.txt --output GCF_013128195.2_ASM1312819v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:25,871] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:25,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d35160b-0547-4802-92ac-9e1efdc8c804/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:25,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d35160b-0547-4802-92ac-9e1efdc8c804/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:25,882] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:25,882] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:25,882] [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
Gemmata obscuriglobus	strain=UQM 2246	GCA_000171775.1	114	114	type	True	79.7825	1253	3285	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_003149495.1	114	114	type	True	79.735	1364	3285	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_008065095.1	114	114	type	True	79.7034	1376	3285	95	below_threshold
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	79.6167	1389	3285	95	below_threshold
Urbifossiella limnaea	strain=ETA_A1	GCA_007747215.1	2528023	2528023	type	True	78.0352	1031	3285	95	below_threshold
Limnoglobus roseus	strain=PX52	GCA_008254045.1	2598579	2598579	type	True	77.1348	723	3285	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	74.9391	85	3285	95	below_threshold
Halorubrum rubrum	strain=YC87	GCA_024494685.1	1126240	1126240	type	True	74.6918	92	3285	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	74.5937	106	3285	95	below_threshold
Halorubrum kocurii	strain=JCM 14978	GCA_000337355.1	478441	478441	type	True	74.5549	92	3285	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:25,884] [INFO] DFAST Taxonomy check result was written to GCF_013128195.2_ASM1312819v2_genomic.fna/tc_result.tsv
[2024-01-24 15:19:25,884] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:25,885] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:25,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d35160b-0547-4802-92ac-9e1efdc8c804/dqc_reference/checkm_data
[2024-01-24 15:19:25,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:25,981] [INFO] Task started: CheckM
[2024-01-24 15:19:25,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013128195.2_ASM1312819v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013128195.2_ASM1312819v2_genomic.fna/checkm_input GCF_013128195.2_ASM1312819v2_genomic.fna/checkm_result
[2024-01-24 15:20:50,663] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:50,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:50,692] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:50,692] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:50,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013128195.2_ASM1312819v2_genomic.fna/markers.fasta)
[2024-01-24 15:20:50,693] [INFO] Task started: Blastn
[2024-01-24 15:20:50,693] [INFO] Running command: blastn -query GCF_013128195.2_ASM1312819v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d35160b-0547-4802-92ac-9e1efdc8c804/dqc_reference/reference_markers_gtdb.fasta -out GCF_013128195.2_ASM1312819v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:51,545] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:51,549] [INFO] Selected 9 target genomes.
[2024-01-24 15:20:51,549] [INFO] Target genome list was writen to GCF_013128195.2_ASM1312819v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:51,557] [INFO] Task started: fastANI
[2024-01-24 15:20:51,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b248ca3-1719-4d0b-b554-093db2d01f55/GCF_013128195.2_ASM1312819v2_genomic.fna.gz --refList GCF_013128195.2_ASM1312819v2_genomic.fna/target_genomes_gtdb.txt --output GCF_013128195.2_ASM1312819v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:13,782] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:13,795] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:13,795] [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_013128195.2	s__Gemmata tundricola	100.0	3282	3285	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017306025.1	s__Gemmata sp017306025	80.9544	1164	3285	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872595.1	s__Gemmata sp016872595	80.2045	1173	3285	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017939745.1	s__Gemmata sp017939745	80.0047	1525	3285	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005773755.1	s__Gemmata sp005773755	79.8571	892	3285	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065095.1	s__Gemmata obscuriglobus	79.7371	1370	3285	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.98	99.95	1.00	1.00	4	-
GCA_000531095.1	s__Gemmata massiliana	79.6777	1353	3285	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	97.81	97.81	0.89	0.89	2	-
GCF_901538265.1	s__Gemmata massiliana_A	79.6558	1411	3285	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005772955.1	s__Gemmata sp005772955	79.0213	1010	3285	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.91	99.90	0.94	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:13,796] [INFO] GTDB search result was written to GCF_013128195.2_ASM1312819v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:13,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:13,804] [INFO] DFAST_QC result json was written to GCF_013128195.2_ASM1312819v2_genomic.fna/dqc_result.json
[2024-01-24 15:21:13,804] [INFO] DFAST_QC completed!
[2024-01-24 15:21:13,804] [INFO] Total running time: 0h2m39s