[2024-01-24 11:26:11,880] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:11,882] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:11,882] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0217200-71d2-44dc-b13e-af60cfbde37c/dqc_reference
[2024-01-24 11:26:13,265] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:13,266] [INFO] Task started: Prodigal
[2024-01-24 11:26:13,266] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c631b1f-3c52-4c6e-8323-3fe519ccfed8/GCF_010894455.1_ASM1089445v1_genomic.fna.gz | prodigal -d GCF_010894455.1_ASM1089445v1_genomic.fna/cds.fna -a GCF_010894455.1_ASM1089445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:55,101] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:55,102] [INFO] Task started: HMMsearch
[2024-01-24 11:26:55,102] [INFO] Running command: hmmsearch --tblout GCF_010894455.1_ASM1089445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0217200-71d2-44dc-b13e-af60cfbde37c/dqc_reference/reference_markers.hmm GCF_010894455.1_ASM1089445v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:55,553] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:55,555] [INFO] Found 6/6 markers.
[2024-01-24 11:26:55,636] [INFO] Query marker FASTA was written to GCF_010894455.1_ASM1089445v1_genomic.fna/markers.fasta
[2024-01-24 11:26:55,637] [INFO] Task started: Blastn
[2024-01-24 11:26:55,637] [INFO] Running command: blastn -query GCF_010894455.1_ASM1089445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0217200-71d2-44dc-b13e-af60cfbde37c/dqc_reference/reference_markers.fasta -out GCF_010894455.1_ASM1089445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:56,343] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:56,347] [INFO] Selected 16 target genomes.
[2024-01-24 11:26:56,347] [INFO] Target genome list was writen to GCF_010894455.1_ASM1089445v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:56,356] [INFO] Task started: fastANI
[2024-01-24 11:26:56,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c631b1f-3c52-4c6e-8323-3fe519ccfed8/GCF_010894455.1_ASM1089445v1_genomic.fna.gz --refList GCF_010894455.1_ASM1089445v1_genomic.fna/target_genomes.txt --output GCF_010894455.1_ASM1089445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:33,416] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:33,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0217200-71d2-44dc-b13e-af60cfbde37c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:33,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0217200-71d2-44dc-b13e-af60cfbde37c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:33,430] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:33,430] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:33,430] [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
Myxococcus eversor	strain=AB053B	GCA_010894455.1	2709661	2709661	type	True	100.0	3751	3754	95	conclusive
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	91.5244	2970	3754	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	87.0259	2821	3754	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	87.0231	2854	3754	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	86.2112	2568	3754	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	83.9894	2461	3754	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	83.9681	2463	3754	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	83.6275	2256	3754	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	81.9009	1881	3754	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	81.8755	1901	3754	95	below_threshold
Megalodesulfovibrio gigas	strain=ATCC 19364	GCA_000468495.1	879	879	type	True	75.0533	87	3754	95	below_threshold
Megalodesulfovibrio gigas	strain=DSM 1382	GCA_000429285.1	879	879	type	True	75.0189	83	3754	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	74.9651	57	3754	95	below_threshold
Actinosynnema mirum	strain=DSM 43827	GCA_000023245.1	40567	40567	type	True	74.8675	387	3754	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	74.8641	371	3754	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	74.8153	346	3754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:33,432] [INFO] DFAST Taxonomy check result was written to GCF_010894455.1_ASM1089445v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:33,432] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:33,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:33,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0217200-71d2-44dc-b13e-af60cfbde37c/dqc_reference/checkm_data
[2024-01-24 11:27:33,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:33,533] [INFO] Task started: CheckM
[2024-01-24 11:27:33,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010894455.1_ASM1089445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010894455.1_ASM1089445v1_genomic.fna/checkm_input GCF_010894455.1_ASM1089445v1_genomic.fna/checkm_result
[2024-01-24 11:31:49,714] [INFO] Task succeeded: CheckM
[2024-01-24 11:31:49,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:31:49,749] [INFO] ===== Completeness check finished =====
[2024-01-24 11:31:49,750] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:31:49,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010894455.1_ASM1089445v1_genomic.fna/markers.fasta)
[2024-01-24 11:31:49,750] [INFO] Task started: Blastn
[2024-01-24 11:31:49,751] [INFO] Running command: blastn -query GCF_010894455.1_ASM1089445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0217200-71d2-44dc-b13e-af60cfbde37c/dqc_reference/reference_markers_gtdb.fasta -out GCF_010894455.1_ASM1089445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:50,900] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:51,182] [INFO] Selected 10 target genomes.
[2024-01-24 11:31:51,183] [INFO] Target genome list was writen to GCF_010894455.1_ASM1089445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:31:51,253] [INFO] Task started: fastANI
[2024-01-24 11:31:51,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c631b1f-3c52-4c6e-8323-3fe519ccfed8/GCF_010894455.1_ASM1089445v1_genomic.fna.gz --refList GCF_010894455.1_ASM1089445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010894455.1_ASM1089445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:32:22,814] [INFO] Task succeeded: fastANI
[2024-01-24 11:32:22,840] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:32:22,840] [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_010894455.1	s__Myxococcus eversor	100.0	3751	3754	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	99.18	99.18	0.94	0.94	2	conclusive
GCF_013336725.1	s__Myxococcus sp013336725	91.6148	3193	3754	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.23	98.12	0.95	0.94	5	-
GCF_900111765.1	s__Myxococcus fulvus	87.028	2853	3754	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.03	95.70	0.96	0.91	4	-
GCF_017301635.1	s__Myxococcus sp017301635	86.241	2575	3754	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331735.1	s__Myxococcus stipitatus	86.206	2570	3754	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010894435.1	s__Myxococcus trucidator	83.978	2464	3754	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010894405.1	s__Myxococcus caerfyrddinensis	83.954	2465	3754	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301735.1	s__Myxococcus sp017301735	83.714	2451	3754	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933655.1	s__Myxococcus fallax	83.6379	2254	3754	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656495.1	s__Myxococcus sp014656495	83.2904	2085	3754	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:32:22,842] [INFO] GTDB search result was written to GCF_010894455.1_ASM1089445v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:32:22,843] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:32:22,848] [INFO] DFAST_QC result json was written to GCF_010894455.1_ASM1089445v1_genomic.fna/dqc_result.json
[2024-01-24 11:32:22,848] [INFO] DFAST_QC completed!
[2024-01-24 11:32:22,848] [INFO] Total running time: 0h6m11s