[2024-01-24 14:55:36,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:36,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:36,584] [INFO] DQC Reference Directory: /var/lib/cwl/stgb61a63ac-8c52-4c84-bd46-f303310c945d/dqc_reference
[2024-01-24 14:55:37,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:37,831] [INFO] Task started: Prodigal
[2024-01-24 14:55:37,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg799e392b-4664-4bc3-9e59-b30a9ab598a8/GCF_028737255.1_ASM2873725v1_genomic.fna.gz | prodigal -d GCF_028737255.1_ASM2873725v1_genomic.fna/cds.fna -a GCF_028737255.1_ASM2873725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:54,082] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:54,082] [INFO] Task started: HMMsearch
[2024-01-24 14:55:54,082] [INFO] Running command: hmmsearch --tblout GCF_028737255.1_ASM2873725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb61a63ac-8c52-4c84-bd46-f303310c945d/dqc_reference/reference_markers.hmm GCF_028737255.1_ASM2873725v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:54,442] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:54,444] [INFO] Found 6/6 markers.
[2024-01-24 14:55:54,504] [INFO] Query marker FASTA was written to GCF_028737255.1_ASM2873725v1_genomic.fna/markers.fasta
[2024-01-24 14:55:54,505] [INFO] Task started: Blastn
[2024-01-24 14:55:54,505] [INFO] Running command: blastn -query GCF_028737255.1_ASM2873725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb61a63ac-8c52-4c84-bd46-f303310c945d/dqc_reference/reference_markers.fasta -out GCF_028737255.1_ASM2873725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:55,993] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:55,996] [INFO] Selected 10 target genomes.
[2024-01-24 14:55:55,997] [INFO] Target genome list was writen to GCF_028737255.1_ASM2873725v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:56,006] [INFO] Task started: fastANI
[2024-01-24 14:55:56,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg799e392b-4664-4bc3-9e59-b30a9ab598a8/GCF_028737255.1_ASM2873725v1_genomic.fna.gz --refList GCF_028737255.1_ASM2873725v1_genomic.fna/target_genomes.txt --output GCF_028737255.1_ASM2873725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:15,821] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:15,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb61a63ac-8c52-4c84-bd46-f303310c945d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:15,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb61a63ac-8c52-4c84-bd46-f303310c945d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:15,831] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:56:15,831] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:56:15,832] [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
Actinomycetospora succinea	strain=DSM 45775	GCA_004363095.1	663603	663603	type	True	87.502	1630	2067	95	below_threshold
Actinomycetospora cinnamomea	strain=DSM 45771	GCA_003096675.1	663609	663609	type	True	86.0215	1472	2067	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	81.2518	1181	2067	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	81.2241	1208	2067	95	below_threshold
Actinomycetospora endophytica	strain=TBRC 5722	GCA_021026375.1	2291215	2291215	type	True	81.0919	1186	2067	95	below_threshold
Actinomycetospora chiangmaiensis	strain=DSM 45062	GCA_000379625.1	402650	402650	type	True	80.993	1167	2067	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	78.1844	955	2067	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	78.0044	894	2067	95	below_threshold
Pseudonocardia hierapolitana	strain=DSM 45671	GCA_007994075.1	1128676	1128676	type	True	77.5324	915	2067	95	below_threshold
Pseudonocardia cypriaca	strain=DSM 45511	GCA_006717045.1	882449	882449	type	True	77.3376	949	2067	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:15,833] [INFO] DFAST Taxonomy check result was written to GCF_028737255.1_ASM2873725v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:15,834] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:15,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:15,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb61a63ac-8c52-4c84-bd46-f303310c945d/dqc_reference/checkm_data
[2024-01-24 14:56:15,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:15,941] [INFO] Task started: CheckM
[2024-01-24 14:56:15,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028737255.1_ASM2873725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028737255.1_ASM2873725v1_genomic.fna/checkm_input GCF_028737255.1_ASM2873725v1_genomic.fna/checkm_result
[2024-01-24 14:57:43,181] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:43,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:43,203] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:43,204] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:43,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028737255.1_ASM2873725v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:43,204] [INFO] Task started: Blastn
[2024-01-24 14:57:43,205] [INFO] Running command: blastn -query GCF_028737255.1_ASM2873725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb61a63ac-8c52-4c84-bd46-f303310c945d/dqc_reference/reference_markers_gtdb.fasta -out GCF_028737255.1_ASM2873725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:45,379] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:45,385] [INFO] Selected 10 target genomes.
[2024-01-24 14:57:45,385] [INFO] Target genome list was writen to GCF_028737255.1_ASM2873725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:45,393] [INFO] Task started: fastANI
[2024-01-24 14:57:45,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg799e392b-4664-4bc3-9e59-b30a9ab598a8/GCF_028737255.1_ASM2873725v1_genomic.fna.gz --refList GCF_028737255.1_ASM2873725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028737255.1_ASM2873725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:03,566] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:03,581] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:58:03,581] [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_004363095.1	s__Actinomycetospora succinea	87.5219	1628	2067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805495.1	s__Actinomycetospora sp902805495	86.3984	961	2067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096675.1	s__Actinomycetospora cinnamomea	86.0029	1475	2067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933465.1	s__Actinomycetospora sp012933465	81.5338	1226	2067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409505.1	s__Actinomycetospora corticicola	81.2578	1178	2067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379625.1	s__Actinomycetospora chiangmaiensis	80.9614	1170	2067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263585.1	s__Pseudonocardia sp019263585	78.1433	963	2067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.90	99.65	0.98	0.94	5	-
GCA_016794615.1	s__Pseudonocardia sp016794615	77.5209	597	2067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994075.1	s__Pseudonocardia hierapolitana	77.5042	925	2067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717045.1	s__Pseudonocardia cypriaca	77.3654	941	2067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:58:03,585] [INFO] GTDB search result was written to GCF_028737255.1_ASM2873725v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:03,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:03,591] [INFO] DFAST_QC result json was written to GCF_028737255.1_ASM2873725v1_genomic.fna/dqc_result.json
[2024-01-24 14:58:03,591] [INFO] DFAST_QC completed!
[2024-01-24 14:58:03,591] [INFO] Total running time: 0h2m27s