[2024-01-24 14:47:08,190] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,192] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,193] [INFO] DQC Reference Directory: /var/lib/cwl/stge030ef98-3c51-4c8a-9966-e396516a977e/dqc_reference
[2024-01-24 14:47:09,687] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:09,688] [INFO] Task started: Prodigal
[2024-01-24 14:47:09,689] [INFO] Running command: gunzip -c /var/lib/cwl/stga1831ce8-c4d4-4c4b-9e00-653b1f409bcd/GCF_009909145.1_ASM990914v1_genomic.fna.gz | prodigal -d GCF_009909145.1_ASM990914v1_genomic.fna/cds.fna -a GCF_009909145.1_ASM990914v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:54,175] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:54,175] [INFO] Task started: HMMsearch
[2024-01-24 14:47:54,175] [INFO] Running command: hmmsearch --tblout GCF_009909145.1_ASM990914v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge030ef98-3c51-4c8a-9966-e396516a977e/dqc_reference/reference_markers.hmm GCF_009909145.1_ASM990914v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:54,637] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:54,638] [INFO] Found 6/6 markers.
[2024-01-24 14:47:54,709] [INFO] Query marker FASTA was written to GCF_009909145.1_ASM990914v1_genomic.fna/markers.fasta
[2024-01-24 14:47:54,710] [INFO] Task started: Blastn
[2024-01-24 14:47:54,710] [INFO] Running command: blastn -query GCF_009909145.1_ASM990914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge030ef98-3c51-4c8a-9966-e396516a977e/dqc_reference/reference_markers.fasta -out GCF_009909145.1_ASM990914v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:55,511] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:55,515] [INFO] Selected 17 target genomes.
[2024-01-24 14:47:55,516] [INFO] Target genome list was writen to GCF_009909145.1_ASM990914v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:55,523] [INFO] Task started: fastANI
[2024-01-24 14:47:55,523] [INFO] Running command: fastANI --query /var/lib/cwl/stga1831ce8-c4d4-4c4b-9e00-653b1f409bcd/GCF_009909145.1_ASM990914v1_genomic.fna.gz --refList GCF_009909145.1_ASM990914v1_genomic.fna/target_genomes.txt --output GCF_009909145.1_ASM990914v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:33,726] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:33,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge030ef98-3c51-4c8a-9966-e396516a977e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:33,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge030ef98-3c51-4c8a-9966-e396516a977e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:33,740] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:33,740] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:33,740] [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
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	100.0	3045	3048	95	conclusive
Corallococcus carmarthensis	strain=CA043D	GCA_003611695.1	2316728	2316728	type	True	90.2729	2341	3048	95	below_threshold
Corallococcus exercitus	strain=AB043A	GCA_003611585.1	2316736	2316736	type	True	90.248	2128	3048	95	below_threshold
Corallococcus aberystwythensis	strain=AB050A	GCA_003612165.1	2316722	2316722	type	True	89.9648	2223	3048	95	below_threshold
Corallococcus coralloides	strain=DSM 2259	GCA_000255295.1	184914	184914	type	True	89.9551	2462	3048	95	below_threshold
Corallococcus exiguus	strain=DSM 14696	GCA_009909105.1	83462	83462	type	True	89.8155	2468	3048	95	below_threshold
Corallococcus interemptor	strain=AB047A	GCA_003668875.1	2316720	2316720	type	True	89.8078	2243	3048	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	89.1352	2264	3048	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	89.0693	1974	3048	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	88.8173	2112	3048	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	88.5987	2161	3048	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.16	360	3048	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.1277	370	3048	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	75.1088	101	3048	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	75.0242	199	3048	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	74.8862	114	3048	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	74.8569	171	3048	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:33,742] [INFO] DFAST Taxonomy check result was written to GCF_009909145.1_ASM990914v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:33,743] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:33,743] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:33,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge030ef98-3c51-4c8a-9966-e396516a977e/dqc_reference/checkm_data
[2024-01-24 14:48:33,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:33,830] [INFO] Task started: CheckM
[2024-01-24 14:48:33,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009909145.1_ASM990914v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009909145.1_ASM990914v1_genomic.fna/checkm_input GCF_009909145.1_ASM990914v1_genomic.fna/checkm_result
[2024-01-24 14:51:47,470] [INFO] Task succeeded: CheckM
[2024-01-24 14:51:47,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:51:47,494] [INFO] ===== Completeness check finished =====
[2024-01-24 14:51:47,494] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:51:47,495] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009909145.1_ASM990914v1_genomic.fna/markers.fasta)
[2024-01-24 14:51:47,495] [INFO] Task started: Blastn
[2024-01-24 14:51:47,495] [INFO] Running command: blastn -query GCF_009909145.1_ASM990914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge030ef98-3c51-4c8a-9966-e396516a977e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009909145.1_ASM990914v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:51:48,808] [INFO] Task succeeded: Blastn
[2024-01-24 14:51:48,811] [INFO] Selected 12 target genomes.
[2024-01-24 14:51:48,811] [INFO] Target genome list was writen to GCF_009909145.1_ASM990914v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:51:48,820] [INFO] Task started: fastANI
[2024-01-24 14:51:48,820] [INFO] Running command: fastANI --query /var/lib/cwl/stga1831ce8-c4d4-4c4b-9e00-653b1f409bcd/GCF_009909145.1_ASM990914v1_genomic.fna.gz --refList GCF_009909145.1_ASM990914v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009909145.1_ASM990914v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:52:23,237] [INFO] Task succeeded: fastANI
[2024-01-24 14:52:23,252] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:52:23,253] [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_009909145.1	s__Corallococcus sp009909145	100.0	3045	3048	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.47	99.47	0.98	0.98	2	conclusive
GCF_003611695.1	s__Corallococcus carmarthensis	90.2896	2337	3048	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611585.1	s__Corallococcus exercitus	90.2477	2128	3048	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	96.95	95.08	0.87	0.82	3	-
GCF_017302985.1	s__Corallococcus macrosporus_A	90.1242	2395	3048	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000255295.1	s__Corallococcus coralloides	89.983	2457	3048	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	95.87	95.41	0.89	0.88	6	-
GCF_003612165.1	s__Corallococcus aberystwythensis	89.9818	2220	3048	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309135.1	s__Corallococcus sp017309135	89.8661	2441	3048	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003668875.1	s__Corallococcus interemptor	89.8379	2238	3048	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.20	99.20	0.95	0.95	2	-
GCF_009909105.1	s__Corallococcus exiguus	89.7972	2471	3048	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	97.29	96.40	0.91	0.89	16	-
GCF_014930455.1	s__Corallococcus sp014930455	89.1588	2259	3048	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611675.1	s__Corallococcus sp003611675	88.8982	2077	3048	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611735.1	s__Corallococcus sicarius	88.8012	2114	3048	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:52:23,254] [INFO] GTDB search result was written to GCF_009909145.1_ASM990914v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:52:23,255] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:52:23,258] [INFO] DFAST_QC result json was written to GCF_009909145.1_ASM990914v1_genomic.fna/dqc_result.json
[2024-01-24 14:52:23,258] [INFO] DFAST_QC completed!
[2024-01-24 14:52:23,259] [INFO] Total running time: 0h5m15s