[2024-01-24 11:34:43,388] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:43,391] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:43,391] [INFO] DQC Reference Directory: /var/lib/cwl/stg96519abf-d805-4b1e-9217-5f4601c7abe5/dqc_reference
[2024-01-24 11:34:44,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,722] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,722] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbf694a4-1d90-426f-8bdd-86416cd9163b/GCF_028368975.1_ASM2836897v1_genomic.fna.gz | prodigal -d GCF_028368975.1_ASM2836897v1_genomic.fna/cds.fna -a GCF_028368975.1_ASM2836897v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:36:10,166] [INFO] Task succeeded: Prodigal
[2024-01-24 11:36:10,167] [INFO] Task started: HMMsearch
[2024-01-24 11:36:10,167] [INFO] Running command: hmmsearch --tblout GCF_028368975.1_ASM2836897v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96519abf-d805-4b1e-9217-5f4601c7abe5/dqc_reference/reference_markers.hmm GCF_028368975.1_ASM2836897v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:36:10,620] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:36:10,622] [INFO] Found 6/6 markers.
[2024-01-24 11:36:10,703] [INFO] Query marker FASTA was written to GCF_028368975.1_ASM2836897v1_genomic.fna/markers.fasta
[2024-01-24 11:36:10,703] [INFO] Task started: Blastn
[2024-01-24 11:36:10,703] [INFO] Running command: blastn -query GCF_028368975.1_ASM2836897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96519abf-d805-4b1e-9217-5f4601c7abe5/dqc_reference/reference_markers.fasta -out GCF_028368975.1_ASM2836897v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:11,484] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:11,487] [INFO] Selected 21 target genomes.
[2024-01-24 11:36:11,488] [INFO] Target genome list was writen to GCF_028368975.1_ASM2836897v1_genomic.fna/target_genomes.txt
[2024-01-24 11:36:11,501] [INFO] Task started: fastANI
[2024-01-24 11:36:11,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbf694a4-1d90-426f-8bdd-86416cd9163b/GCF_028368975.1_ASM2836897v1_genomic.fna.gz --refList GCF_028368975.1_ASM2836897v1_genomic.fna/target_genomes.txt --output GCF_028368975.1_ASM2836897v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:47,546] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:47,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96519abf-d805-4b1e-9217-5f4601c7abe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:47,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96519abf-d805-4b1e-9217-5f4601c7abe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:47,574] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:36:47,574] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:36:47,575] [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
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	87.8794	2561	3649	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	87.8656	2503	3649	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	87.8591	2510	3649	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	80.1872	1220	3649	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	80.0992	1489	3649	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	80.0888	1529	3649	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	80.0689	1522	3649	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	80.0242	1300	3649	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	80.0139	1490	3649	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	79.9998	1346	3649	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	79.8736	1341	3649	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	79.8253	1355	3649	95	below_threshold
Desulfohalovibrio reitneri	strain=L21-Syr-AB	GCA_000711295.1	1307759	1307759	type	True	75.5376	91	3649	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_001399755.1	381306	381306	type	True	75.437	115	3649	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_900101365.1	381306	381306	type	True	75.335	114	3649	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.3251	316	3649	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.1673	302	3649	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	75.1002	273	3649	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_003149495.1	114	114	type	True	74.9349	145	3649	95	below_threshold
Gemmata obscuriglobus	strain=UQM 2246	GCA_000171775.1	114	114	type	True	74.9299	139	3649	95	below_threshold
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	74.9255	146	3649	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:47,577] [INFO] DFAST Taxonomy check result was written to GCF_028368975.1_ASM2836897v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:47,577] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:47,577] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:47,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96519abf-d805-4b1e-9217-5f4601c7abe5/dqc_reference/checkm_data
[2024-01-24 11:36:47,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:47,675] [INFO] Task started: CheckM
[2024-01-24 11:36:47,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028368975.1_ASM2836897v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028368975.1_ASM2836897v1_genomic.fna/checkm_input GCF_028368975.1_ASM2836897v1_genomic.fna/checkm_result
[2024-01-24 11:42:34,198] [INFO] Task succeeded: CheckM
[2024-01-24 11:42:34,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:42:34,228] [INFO] ===== Completeness check finished =====
[2024-01-24 11:42:34,228] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:42:34,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028368975.1_ASM2836897v1_genomic.fna/markers.fasta)
[2024-01-24 11:42:34,230] [INFO] Task started: Blastn
[2024-01-24 11:42:34,230] [INFO] Running command: blastn -query GCF_028368975.1_ASM2836897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96519abf-d805-4b1e-9217-5f4601c7abe5/dqc_reference/reference_markers_gtdb.fasta -out GCF_028368975.1_ASM2836897v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:35,551] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:35,598] [INFO] Selected 8 target genomes.
[2024-01-24 11:42:35,598] [INFO] Target genome list was writen to GCF_028368975.1_ASM2836897v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:42:35,754] [INFO] Task started: fastANI
[2024-01-24 11:42:35,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbf694a4-1d90-426f-8bdd-86416cd9163b/GCF_028368975.1_ASM2836897v1_genomic.fna.gz --refList GCF_028368975.1_ASM2836897v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028368975.1_ASM2836897v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:42:56,797] [INFO] Task succeeded: fastANI
[2024-01-24 11:42:56,813] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:42:56,813] [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_000165485.1	s__Stigmatella aurantiaca_A	91.3155	2901	3649	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900111745.1	s__Stigmatella erecta	87.8934	2558	3649	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.281	N/A	N/A	N/A	N/A	1	-
GCF_900109545.1	s__Stigmatella aurantiaca	87.8518	2511	3649	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.281	N/A	N/A	N/A	N/A	1	-
GCA_016926755.1	s__Hyalangium sp016926755	82.5631	1540	3649	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Hyalangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737315.1	s__Hyalangium minutum	81.5877	1806	3649	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Hyalangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016859125.1	s__Archangium violaceum_A	80.2304	1502	3649	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027285.1	s__Archangium gephyra	80.0877	1487	3649	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900111765.1	s__Myxococcus fulvus	79.8386	1353	3649	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.03	95.70	0.96	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:42:56,816] [INFO] GTDB search result was written to GCF_028368975.1_ASM2836897v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:42:56,816] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:42:56,822] [INFO] DFAST_QC result json was written to GCF_028368975.1_ASM2836897v1_genomic.fna/dqc_result.json
[2024-01-24 11:42:56,823] [INFO] DFAST_QC completed!
[2024-01-24 11:42:56,823] [INFO] Total running time: 0h8m13s