[2024-01-24 14:23:03,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:03,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:03,969] [INFO] DQC Reference Directory: /var/lib/cwl/stgdde708d8-8850-4ccb-8e0c-653048297b5d/dqc_reference
[2024-01-24 14:23:05,352] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:05,353] [INFO] Task started: Prodigal
[2024-01-24 14:23:05,354] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dc49c99-5fea-4035-ad79-d68830e25c7c/GCF_007989405.1_ASM798940v1_genomic.fna.gz | prodigal -d GCF_007989405.1_ASM798940v1_genomic.fna/cds.fna -a GCF_007989405.1_ASM798940v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:47,942] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:47,943] [INFO] Task started: HMMsearch
[2024-01-24 14:23:47,943] [INFO] Running command: hmmsearch --tblout GCF_007989405.1_ASM798940v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdde708d8-8850-4ccb-8e0c-653048297b5d/dqc_reference/reference_markers.hmm GCF_007989405.1_ASM798940v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:48,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:48,403] [INFO] Found 6/6 markers.
[2024-01-24 14:23:48,481] [INFO] Query marker FASTA was written to GCF_007989405.1_ASM798940v1_genomic.fna/markers.fasta
[2024-01-24 14:23:48,482] [INFO] Task started: Blastn
[2024-01-24 14:23:48,482] [INFO] Running command: blastn -query GCF_007989405.1_ASM798940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdde708d8-8850-4ccb-8e0c-653048297b5d/dqc_reference/reference_markers.fasta -out GCF_007989405.1_ASM798940v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:49,234] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:49,237] [INFO] Selected 15 target genomes.
[2024-01-24 14:23:49,238] [INFO] Target genome list was writen to GCF_007989405.1_ASM798940v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:49,243] [INFO] Task started: fastANI
[2024-01-24 14:23:49,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dc49c99-5fea-4035-ad79-d68830e25c7c/GCF_007989405.1_ASM798940v1_genomic.fna.gz --refList GCF_007989405.1_ASM798940v1_genomic.fna/target_genomes.txt --output GCF_007989405.1_ASM798940v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:24:17,175] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:17,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdde708d8-8850-4ccb-8e0c-653048297b5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:24:17,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdde708d8-8850-4ccb-8e0c-653048297b5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:24:17,192] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:24:17,193] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:24:17,193] [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 virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	100.0	2969	2975	95	inconclusive
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	99.9989	2966	2975	95	inconclusive
Myxococcus xanthus	strain=DSM 16526	GCA_900106535.1	34	34	type	True	96.8306	2711	2975	95	inconclusive
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	93.5858	2102	2975	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	84.6811	2145	2975	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	84.6015	2106	2975	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	84.5882	1958	2975	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	82.1744	1714	2975	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	82.1267	1635	2975	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	75.0065	99	2975	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	74.9959	79	2975	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	74.9888	80	2975	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	74.9885	80	2975	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	74.9801	104	2975	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	74.867	173	2975	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:24:17,194] [INFO] DFAST Taxonomy check result was written to GCF_007989405.1_ASM798940v1_genomic.fna/tc_result.tsv
[2024-01-24 14:24:17,195] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:24:17,195] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:24:17,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdde708d8-8850-4ccb-8e0c-653048297b5d/dqc_reference/checkm_data
[2024-01-24 14:24:17,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:24:17,277] [INFO] Task started: CheckM
[2024-01-24 14:24:17,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989405.1_ASM798940v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989405.1_ASM798940v1_genomic.fna/checkm_input GCF_007989405.1_ASM798940v1_genomic.fna/checkm_result
[2024-01-24 14:27:07,124] [INFO] Task succeeded: CheckM
[2024-01-24 14:27:07,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:27:07,152] [INFO] ===== Completeness check finished =====
[2024-01-24 14:27:07,152] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:27:07,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989405.1_ASM798940v1_genomic.fna/markers.fasta)
[2024-01-24 14:27:07,154] [INFO] Task started: Blastn
[2024-01-24 14:27:07,154] [INFO] Running command: blastn -query GCF_007989405.1_ASM798940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdde708d8-8850-4ccb-8e0c-653048297b5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989405.1_ASM798940v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:27:08,198] [INFO] Task succeeded: Blastn
[2024-01-24 14:27:08,202] [INFO] Selected 6 target genomes.
[2024-01-24 14:27:08,202] [INFO] Target genome list was writen to GCF_007989405.1_ASM798940v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:27:08,216] [INFO] Task started: fastANI
[2024-01-24 14:27:08,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dc49c99-5fea-4035-ad79-d68830e25c7c/GCF_007989405.1_ASM798940v1_genomic.fna.gz --refList GCF_007989405.1_ASM798940v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989405.1_ASM798940v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:27:23,280] [INFO] Task succeeded: fastANI
[2024-01-24 14:27:23,289] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:27:23,289] [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_900101905.1	s__Myxococcus virescens	99.9941	2967	2975	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.8216	98.11	97.12	0.95	0.93	4	conclusive
GCF_900106535.1	s__Myxococcus xanthus	96.8161	2713	2975	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.8216	99.36	96.84	0.98	0.91	10	-
GCF_013116825.1	s__Myxococcus xanthus_B	96.628	2535	2975	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.6332	99.98	99.98	0.98	0.98	2	-
GCF_010998615.1	s__Myxococcus sp010998615	96.3366	2596	2975	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.6778	99.99	99.99	0.99	0.99	9	-
GCF_006402735.1	s__Myxococcus xanthus_A	95.8328	2649	2975	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.2302	99.44	99.22	0.98	0.96	5	-
GCF_002305895.1	s__Myxococcus macrosporus	91.3205	2479	2975	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.54	98.54	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:27:23,291] [INFO] GTDB search result was written to GCF_007989405.1_ASM798940v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:27:23,291] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:27:23,323] [INFO] DFAST_QC result json was written to GCF_007989405.1_ASM798940v1_genomic.fna/dqc_result.json
[2024-01-24 14:27:23,323] [INFO] DFAST_QC completed!
[2024-01-24 14:27:23,323] [INFO] Total running time: 0h4m19s