[2024-01-25 19:55:20,794] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:20,797] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:20,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bd62135-4da5-4a0c-8407-bb3f41fcf863/dqc_reference
[2024-01-25 19:55:21,984] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:21,986] [INFO] Task started: Prodigal
[2024-01-25 19:55:21,986] [INFO] Running command: gunzip -c /var/lib/cwl/stg83d6933e-06b5-4a75-9b09-4c0810afb2a1/GCF_014672695.1_ASM1467269v1_genomic.fna.gz | prodigal -d GCF_014672695.1_ASM1467269v1_genomic.fna/cds.fna -a GCF_014672695.1_ASM1467269v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:33,729] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:33,730] [INFO] Task started: HMMsearch
[2024-01-25 19:55:33,730] [INFO] Running command: hmmsearch --tblout GCF_014672695.1_ASM1467269v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bd62135-4da5-4a0c-8407-bb3f41fcf863/dqc_reference/reference_markers.hmm GCF_014672695.1_ASM1467269v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:34,032] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:34,033] [INFO] Found 6/6 markers.
[2024-01-25 19:55:34,067] [INFO] Query marker FASTA was written to GCF_014672695.1_ASM1467269v1_genomic.fna/markers.fasta
[2024-01-25 19:55:34,068] [INFO] Task started: Blastn
[2024-01-25 19:55:34,068] [INFO] Running command: blastn -query GCF_014672695.1_ASM1467269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bd62135-4da5-4a0c-8407-bb3f41fcf863/dqc_reference/reference_markers.fasta -out GCF_014672695.1_ASM1467269v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:34,830] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:34,834] [INFO] Selected 24 target genomes.
[2024-01-25 19:55:34,834] [INFO] Target genome list was writen to GCF_014672695.1_ASM1467269v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:34,863] [INFO] Task started: fastANI
[2024-01-25 19:55:34,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg83d6933e-06b5-4a75-9b09-4c0810afb2a1/GCF_014672695.1_ASM1467269v1_genomic.fna.gz --refList GCF_014672695.1_ASM1467269v1_genomic.fna/target_genomes.txt --output GCF_014672695.1_ASM1467269v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:59,669] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:59,670] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bd62135-4da5-4a0c-8407-bb3f41fcf863/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:59,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bd62135-4da5-4a0c-8407-bb3f41fcf863/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:59,683] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:55:59,683] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:59,684] [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
Defluviicoccus vanus	strain=Ben 114	GCA_014672695.1	111831	111831	type	True	100.0	1408	1408	95	conclusive
Rhizobium subbaraonis	strain=JC85	GCA_900220975.1	908946	908946	type	True	76.9615	111	1408	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.9177	104	1408	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	76.6706	50	1408	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.665	160	1408	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.6058	159	1408	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	76.5515	92	1408	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.4003	102	1408	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.3859	122	1408	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.3528	198	1408	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.3093	123	1408	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.2961	143	1408	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.2941	164	1408	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.2732	172	1408	95	below_threshold
Aureimonas phyllosphaerae	strain=DSM 25024	GCA_014196405.1	1166078	1166078	type	True	76.2694	74	1408	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.2351	205	1408	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.1734	167	1408	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.1685	122	1408	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.1649	200	1408	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.1343	132	1408	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.1294	163	1408	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.077	114	1408	95	below_threshold
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	75.6873	131	1408	95	below_threshold
Denitrobaculum tricleocarpae	strain=R148	GCA_007004665.1	2591009	2591009	type	True	75.6051	68	1408	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:59,685] [INFO] DFAST Taxonomy check result was written to GCF_014672695.1_ASM1467269v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:59,685] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:59,686] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:59,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bd62135-4da5-4a0c-8407-bb3f41fcf863/dqc_reference/checkm_data
[2024-01-25 19:55:59,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:59,728] [INFO] Task started: CheckM
[2024-01-25 19:55:59,728] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014672695.1_ASM1467269v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014672695.1_ASM1467269v1_genomic.fna/checkm_input GCF_014672695.1_ASM1467269v1_genomic.fna/checkm_result
[2024-01-25 19:56:35,089] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:35,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:35,107] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:35,107] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:35,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014672695.1_ASM1467269v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:35,108] [INFO] Task started: Blastn
[2024-01-25 19:56:35,108] [INFO] Running command: blastn -query GCF_014672695.1_ASM1467269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bd62135-4da5-4a0c-8407-bb3f41fcf863/dqc_reference/reference_markers_gtdb.fasta -out GCF_014672695.1_ASM1467269v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:36,297] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:36,300] [INFO] Selected 17 target genomes.
[2024-01-25 19:56:36,301] [INFO] Target genome list was writen to GCF_014672695.1_ASM1467269v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:36,331] [INFO] Task started: fastANI
[2024-01-25 19:56:36,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg83d6933e-06b5-4a75-9b09-4c0810afb2a1/GCF_014672695.1_ASM1467269v1_genomic.fna.gz --refList GCF_014672695.1_ASM1467269v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014672695.1_ASM1467269v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:51,748] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:51,759] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:51,760] [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_014672695.1	s__Defluviicoccus vanus	100.0	1408	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__Defluviicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016712375.1	s__SSA4 sp016712375	78.2764	274	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013414705.1	s__SSA4 sp013414705	78.2714	319	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712595.1	s__SSA4 sp016712595	78.2257	297	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793875.1	s__SSA4 sp016793875	77.9742	289	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900609035.2	s__Defluviicoccus_A seviourii	77.1396	216	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__Defluviicoccus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793925.1	s__JAEULH01 sp016793925	77.0952	213	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__JAEULH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694935.1	s__REEP01 sp007694935	77.0503	162	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__REEP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900220975.1	s__Mycoplana subbaraonis	76.943	113	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	76.6513	161	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.6232	167	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007695045.1	s__REEP01 sp007695045	76.4332	149	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__REEP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729425.1	s__Phaeospirillum sp902729425	76.3462	127	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	76.1424	172	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432935.1	s__JAHDSF01 sp018432935	76.1194	137	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643375.1	s__Aureimonas_A glaciei	76.0858	128	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691105.1	s__SHVU01 sp009691105	75.8126	56	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__SHVU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:51,761] [INFO] GTDB search result was written to GCF_014672695.1_ASM1467269v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:51,761] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:51,765] [INFO] DFAST_QC result json was written to GCF_014672695.1_ASM1467269v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:51,765] [INFO] DFAST_QC completed!
[2024-01-25 19:56:51,765] [INFO] Total running time: 0h1m31s