[2023-06-27 06:26:22,594] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:26:22,596] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:26:22,596] [INFO] DQC Reference Directory: /var/lib/cwl/stg3103573a-b231-4278-b8ac-1bd3cb935788/dqc_reference
[2023-06-27 06:26:23,837] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:26:23,837] [INFO] Task started: Prodigal
[2023-06-27 06:26:23,838] [INFO] Running command: gunzip -c /var/lib/cwl/stgcedd5083-c5cd-4caf-b352-4db75e016e72/GCA_026705295.1_ASM2670529v1_genomic.fna.gz | prodigal -d GCA_026705295.1_ASM2670529v1_genomic.fna/cds.fna -a GCA_026705295.1_ASM2670529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:26:32,731] [INFO] Task succeeded: Prodigal
[2023-06-27 06:26:32,732] [INFO] Task started: HMMsearch
[2023-06-27 06:26:32,732] [INFO] Running command: hmmsearch --tblout GCA_026705295.1_ASM2670529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3103573a-b231-4278-b8ac-1bd3cb935788/dqc_reference/reference_markers.hmm GCA_026705295.1_ASM2670529v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:26:33,065] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:26:33,067] [INFO] Found 6/6 markers.
[2023-06-27 06:26:33,099] [INFO] Query marker FASTA was written to GCA_026705295.1_ASM2670529v1_genomic.fna/markers.fasta
[2023-06-27 06:26:33,100] [INFO] Task started: Blastn
[2023-06-27 06:26:33,100] [INFO] Running command: blastn -query GCA_026705295.1_ASM2670529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3103573a-b231-4278-b8ac-1bd3cb935788/dqc_reference/reference_markers.fasta -out GCA_026705295.1_ASM2670529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:26:33,790] [INFO] Task succeeded: Blastn
[2023-06-27 06:26:33,795] [INFO] Selected 26 target genomes.
[2023-06-27 06:26:33,796] [INFO] Target genome list was writen to GCA_026705295.1_ASM2670529v1_genomic.fna/target_genomes.txt
[2023-06-27 06:26:33,800] [INFO] Task started: fastANI
[2023-06-27 06:26:33,800] [INFO] Running command: fastANI --query /var/lib/cwl/stgcedd5083-c5cd-4caf-b352-4db75e016e72/GCA_026705295.1_ASM2670529v1_genomic.fna.gz --refList GCA_026705295.1_ASM2670529v1_genomic.fna/target_genomes.txt --output GCA_026705295.1_ASM2670529v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:26:57,598] [INFO] Task succeeded: fastANI
[2023-06-27 06:26:57,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3103573a-b231-4278-b8ac-1bd3cb935788/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:26:57,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3103573a-b231-4278-b8ac-1bd3cb935788/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:26:57,616] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:26:57,616] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 06:26:57,616] [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
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.3712	92	1099	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.3026	90	1099	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.2937	91	1099	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.2411	168	1099	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	75.0016	52	1099	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	74.9813	63	1099	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	74.8913	99	1099	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	74.8533	57	1099	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	74.8376	94	1099	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	74.8364	60	1099	95	below_threshold
Cnuibacter physcomitrellae	strain=XA(T)	GCA_002096055.1	1619308	1619308	type	True	74.8328	61	1099	95	below_threshold
Halegenticoccus soli	strain=SYSU A9-0	GCA_002844195.1	1985678	1985678	type	True	74.7755	51	1099	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	74.7707	51	1099	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.7582	110	1099	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	74.7545	103	1099	95	below_threshold
Streptomyces goshikiensis	strain=JCM 4640	GCA_014650555.1	1942	1942	type	True	74.7401	111	1099	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	74.6899	92	1099	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.6579	121	1099	95	below_threshold
Fimbriiglobus ruber	strain=SP5	GCA_002197845.1	1908690	1908690	type	True	74.6318	69	1099	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	74.5448	57	1099	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	74.5415	54	1099	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 06:26:57,618] [INFO] DFAST Taxonomy check result was written to GCA_026705295.1_ASM2670529v1_genomic.fna/tc_result.tsv
[2023-06-27 06:26:57,619] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:26:57,619] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:26:57,619] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3103573a-b231-4278-b8ac-1bd3cb935788/dqc_reference/checkm_data
[2023-06-27 06:26:57,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:26:57,679] [INFO] Task started: CheckM
[2023-06-27 06:26:57,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026705295.1_ASM2670529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026705295.1_ASM2670529v1_genomic.fna/checkm_input GCA_026705295.1_ASM2670529v1_genomic.fna/checkm_result
[2023-06-27 06:27:29,630] [INFO] Task succeeded: CheckM
[2023-06-27 06:27:29,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:27:29,654] [INFO] ===== Completeness check finished =====
[2023-06-27 06:27:29,654] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:27:29,655] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026705295.1_ASM2670529v1_genomic.fna/markers.fasta)
[2023-06-27 06:27:29,655] [INFO] Task started: Blastn
[2023-06-27 06:27:29,655] [INFO] Running command: blastn -query GCA_026705295.1_ASM2670529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3103573a-b231-4278-b8ac-1bd3cb935788/dqc_reference/reference_markers_gtdb.fasta -out GCA_026705295.1_ASM2670529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:27:30,625] [INFO] Task succeeded: Blastn
[2023-06-27 06:27:30,629] [INFO] Selected 5 target genomes.
[2023-06-27 06:27:30,629] [INFO] Target genome list was writen to GCA_026705295.1_ASM2670529v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:27:30,631] [INFO] Task started: fastANI
[2023-06-27 06:27:30,632] [INFO] Running command: fastANI --query /var/lib/cwl/stgcedd5083-c5cd-4caf-b352-4db75e016e72/GCA_026705295.1_ASM2670529v1_genomic.fna.gz --refList GCA_026705295.1_ASM2670529v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026705295.1_ASM2670529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:27:35,088] [INFO] Task succeeded: fastANI
[2023-06-27 06:27:35,098] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:27:35,098] [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
GCA_009840115.1	s__JAAXHJ01 sp009840115	92.2866	925	1099	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	99.91	99.91	0.95	0.95	2	-
GCA_009841015.1	s__JAAXHJ01 sp009841015	91.6786	881	1099	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009838765.1	s__JAAXHJ01 sp009838765	91.3711	922	1099	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	99.96	99.96	0.97	0.96	3	-
GCA_009841005.1	s__JAAXHJ01 sp009841005	90.0009	841	1099	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	96.67	96.60	0.84	0.81	5	-
GCA_012270965.1	s__JAAXHJ01 sp012270965	88.8312	862	1099	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:27:35,100] [INFO] GTDB search result was written to GCA_026705295.1_ASM2670529v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:27:35,100] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:27:35,114] [INFO] DFAST_QC result json was written to GCA_026705295.1_ASM2670529v1_genomic.fna/dqc_result.json
[2023-06-27 06:27:35,115] [INFO] DFAST_QC completed!
[2023-06-27 06:27:35,115] [INFO] Total running time: 0h1m13s