[2024-01-24 12:54:39,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:39,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:39,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg6578d39b-66a1-4f52-9904-61c817ba3901/dqc_reference
[2024-01-24 12:54:40,994] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:40,995] [INFO] Task started: Prodigal
[2024-01-24 12:54:40,995] [INFO] Running command: gunzip -c /var/lib/cwl/stg10fb30ab-1db0-44cb-a659-9c05257ab058/GCF_019797865.1_ASM1979786v1_genomic.fna.gz | prodigal -d GCF_019797865.1_ASM1979786v1_genomic.fna/cds.fna -a GCF_019797865.1_ASM1979786v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:56,406] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:56,406] [INFO] Task started: HMMsearch
[2024-01-24 12:54:56,407] [INFO] Running command: hmmsearch --tblout GCF_019797865.1_ASM1979786v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6578d39b-66a1-4f52-9904-61c817ba3901/dqc_reference/reference_markers.hmm GCF_019797865.1_ASM1979786v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:56,738] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:56,740] [INFO] Found 6/6 markers.
[2024-01-24 12:54:56,796] [INFO] Query marker FASTA was written to GCF_019797865.1_ASM1979786v1_genomic.fna/markers.fasta
[2024-01-24 12:54:56,797] [INFO] Task started: Blastn
[2024-01-24 12:54:56,797] [INFO] Running command: blastn -query GCF_019797865.1_ASM1979786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6578d39b-66a1-4f52-9904-61c817ba3901/dqc_reference/reference_markers.fasta -out GCF_019797865.1_ASM1979786v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:57,777] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:57,783] [INFO] Selected 33 target genomes.
[2024-01-24 12:54:57,783] [INFO] Target genome list was writen to GCF_019797865.1_ASM1979786v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:57,795] [INFO] Task started: fastANI
[2024-01-24 12:54:57,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg10fb30ab-1db0-44cb-a659-9c05257ab058/GCF_019797865.1_ASM1979786v1_genomic.fna.gz --refList GCF_019797865.1_ASM1979786v1_genomic.fna/target_genomes.txt --output GCF_019797865.1_ASM1979786v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:30,165] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:30,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6578d39b-66a1-4f52-9904-61c817ba3901/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:30,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6578d39b-66a1-4f52-9904-61c817ba3901/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:30,195] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:55:30,196] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:55:30,196] [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
Hansschlegelia beijingensis	strain=DSM 25481	GCA_014196425.1	1133344	1133344	type	True	81.3817	769	1847	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	78.2334	535	1847	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	77.8597	495	1847	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	77.8163	570	1847	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.7972	472	1847	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	77.796	546	1847	95	below_threshold
Methylobacterium radiodurans	strain=17Sr1-43	GCA_003173735.1	2202828	2202828	type	True	77.7822	537	1847	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.6741	429	1847	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.6594	346	1847	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.6538	582	1847	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.633	432	1847	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	77.6259	568	1847	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	77.5811	592	1847	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	77.5749	554	1847	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.5441	469	1847	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	77.5383	401	1847	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	77.5238	341	1847	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	77.5168	536	1847	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	77.5127	340	1847	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	77.4952	308	1847	95	below_threshold
Bradyrhizobium mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	77.4932	467	1847	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	77.4929	568	1847	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.463	490	1847	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	77.457	443	1847	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	77.3734	557	1847	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	77.3493	493	1847	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	77.3418	560	1847	95	below_threshold
Methylobacterium brachiatum	strain=B0021	GCA_020523825.1	269660	269660	type	True	77.3193	488	1847	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	77.2964	607	1847	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	77.2034	473	1847	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	77.1471	351	1847	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	77.0922	484	1847	95	below_threshold
Arsenicitalea aurantiaca	strain=42-50	GCA_003994485.1	1783274	1783274	type	True	76.6786	218	1847	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:30,198] [INFO] DFAST Taxonomy check result was written to GCF_019797865.1_ASM1979786v1_genomic.fna/tc_result.tsv
[2024-01-24 12:55:30,199] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:30,199] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:30,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6578d39b-66a1-4f52-9904-61c817ba3901/dqc_reference/checkm_data
[2024-01-24 12:55:30,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:30,252] [INFO] Task started: CheckM
[2024-01-24 12:55:30,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019797865.1_ASM1979786v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019797865.1_ASM1979786v1_genomic.fna/checkm_input GCF_019797865.1_ASM1979786v1_genomic.fna/checkm_result
[2024-01-24 12:56:13,811] [INFO] Task succeeded: CheckM
[2024-01-24 12:56:13,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:56:13,836] [INFO] ===== Completeness check finished =====
[2024-01-24 12:56:13,836] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:56:13,837] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019797865.1_ASM1979786v1_genomic.fna/markers.fasta)
[2024-01-24 12:56:13,837] [INFO] Task started: Blastn
[2024-01-24 12:56:13,837] [INFO] Running command: blastn -query GCF_019797865.1_ASM1979786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6578d39b-66a1-4f52-9904-61c817ba3901/dqc_reference/reference_markers_gtdb.fasta -out GCF_019797865.1_ASM1979786v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:56:15,507] [INFO] Task succeeded: Blastn
[2024-01-24 12:56:15,511] [INFO] Selected 7 target genomes.
[2024-01-24 12:56:15,511] [INFO] Target genome list was writen to GCF_019797865.1_ASM1979786v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:56:15,517] [INFO] Task started: fastANI
[2024-01-24 12:56:15,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg10fb30ab-1db0-44cb-a659-9c05257ab058/GCF_019797865.1_ASM1979786v1_genomic.fna.gz --refList GCF_019797865.1_ASM1979786v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019797865.1_ASM1979786v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:23,399] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:23,410] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:56:23,410] [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_003241695.1	s__Hansschlegelia sp003241695	85.0449	1067	1847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004103825.1	s__Hansschlegelia zhihuaiae	83.4326	1015	1847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168115.1	s__Hansschlegelia sp902168115	83.0696	942	1847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384475.1	s__Hansschlegelia sp000384475	82.7846	992	1847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196425.1	s__Hansschlegelia beijingensis	81.3493	773	1847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526315.1	s__Methylopila sp000526315	81.1431	890	1847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310425.1	s__Hansschlegelia quercus	80.9465	778	1847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:23,412] [INFO] GTDB search result was written to GCF_019797865.1_ASM1979786v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:23,413] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:23,421] [INFO] DFAST_QC result json was written to GCF_019797865.1_ASM1979786v1_genomic.fna/dqc_result.json
[2024-01-24 12:56:23,421] [INFO] DFAST_QC completed!
[2024-01-24 12:56:23,421] [INFO] Total running time: 0h1m44s