[2024-01-24 11:58:55,858] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:55,860] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:55,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e427c95-ad38-490c-a69f-7af946a06a39/dqc_reference
[2024-01-24 11:58:57,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:57,127] [INFO] Task started: Prodigal
[2024-01-24 11:58:57,127] [INFO] Running command: gunzip -c /var/lib/cwl/stg1eb38112-8f15-4f62-974a-3148a11c2bda/GCF_012584515.1_ASM1258451v1_genomic.fna.gz | prodigal -d GCF_012584515.1_ASM1258451v1_genomic.fna/cds.fna -a GCF_012584515.1_ASM1258451v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:08,107] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:08,108] [INFO] Task started: HMMsearch
[2024-01-24 11:59:08,108] [INFO] Running command: hmmsearch --tblout GCF_012584515.1_ASM1258451v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e427c95-ad38-490c-a69f-7af946a06a39/dqc_reference/reference_markers.hmm GCF_012584515.1_ASM1258451v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:08,441] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:08,442] [INFO] Found 6/6 markers.
[2024-01-24 11:59:08,474] [INFO] Query marker FASTA was written to GCF_012584515.1_ASM1258451v1_genomic.fna/markers.fasta
[2024-01-24 11:59:08,474] [INFO] Task started: Blastn
[2024-01-24 11:59:08,475] [INFO] Running command: blastn -query GCF_012584515.1_ASM1258451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e427c95-ad38-490c-a69f-7af946a06a39/dqc_reference/reference_markers.fasta -out GCF_012584515.1_ASM1258451v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:09,130] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:09,134] [INFO] Selected 22 target genomes.
[2024-01-24 11:59:09,135] [INFO] Target genome list was writen to GCF_012584515.1_ASM1258451v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:09,160] [INFO] Task started: fastANI
[2024-01-24 11:59:09,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eb38112-8f15-4f62-974a-3148a11c2bda/GCF_012584515.1_ASM1258451v1_genomic.fna.gz --refList GCF_012584515.1_ASM1258451v1_genomic.fna/target_genomes.txt --output GCF_012584515.1_ASM1258451v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:26,957] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:26,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e427c95-ad38-490c-a69f-7af946a06a39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:26,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e427c95-ad38-490c-a69f-7af946a06a39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:26,973] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:26,974] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:26,974] [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
Polaromonas vacuolata	strain=KCTC 22033	GCA_012584515.1	37448	37448	type	True	100.0	1273	1279	95	conclusive
Polaromonas naphthalenivorans	strain=CJ2	GCA_000015505.1	216465	216465	type	True	77.5619	264	1279	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	77.3473	286	1279	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	77.3133	143	1279	95	below_threshold
Polaromonas eurypsychrophila	strain=CGMCC 1.15322	GCA_014641715.1	1614635	1614635	type	True	77.2334	226	1279	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	77.2082	140	1279	95	below_threshold
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001761385.1	1763535	1763535	type	True	77.0477	120	1279	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	76.8483	137	1279	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	76.7321	122	1279	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	76.7309	128	1279	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	76.6903	152	1279	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	76.5378	122	1279	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	76.4622	64	1279	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	76.4029	104	1279	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	76.3905	128	1279	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	76.336	129	1279	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	76.2989	115	1279	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	76.1254	130	1279	95	below_threshold
Serpentinimonas barnesii	strain=H1	GCA_000696225.1	1458427	1458427	type	True	76.0742	83	1279	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	75.9926	112	1279	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:26,977] [INFO] DFAST Taxonomy check result was written to GCF_012584515.1_ASM1258451v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:26,978] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:26,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:26,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e427c95-ad38-490c-a69f-7af946a06a39/dqc_reference/checkm_data
[2024-01-24 11:59:26,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:27,019] [INFO] Task started: CheckM
[2024-01-24 11:59:27,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012584515.1_ASM1258451v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012584515.1_ASM1258451v1_genomic.fna/checkm_input GCF_012584515.1_ASM1258451v1_genomic.fna/checkm_result
[2024-01-24 12:00:03,834] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:03,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:03,853] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:03,854] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:03,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012584515.1_ASM1258451v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:03,854] [INFO] Task started: Blastn
[2024-01-24 12:00:03,855] [INFO] Running command: blastn -query GCF_012584515.1_ASM1258451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e427c95-ad38-490c-a69f-7af946a06a39/dqc_reference/reference_markers_gtdb.fasta -out GCF_012584515.1_ASM1258451v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:05,004] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:05,014] [INFO] Selected 20 target genomes.
[2024-01-24 12:00:05,015] [INFO] Target genome list was writen to GCF_012584515.1_ASM1258451v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:05,050] [INFO] Task started: fastANI
[2024-01-24 12:00:05,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eb38112-8f15-4f62-974a-3148a11c2bda/GCF_012584515.1_ASM1258451v1_genomic.fna.gz --refList GCF_012584515.1_ASM1258451v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012584515.1_ASM1258451v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:20,335] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:20,350] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:20,351] [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_012584515.1	s__Polaromonas vacuolata	100.0	1267	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112285.1	s__Polaromonas sp900112285	77.8724	308	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688115.1	s__Polaromonas sp000688115	77.7598	234	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116715.1	s__Polaromonas sp900116715	77.7045	285	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185115.1	s__Polaromonas sp016185115	77.6538	251	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002379085.1	s__Polaromonas sp002379085	77.5288	247	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711205.1	s__Polaromonas sp003711205	77.4989	279	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000013865.1	s__Polaromonas sp000013865	77.4915	257	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000709345.1	s__Polaromonas glacialis	77.4783	253	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002379095.1	s__Polaromonas sp002379095	77.4564	234	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780625.1	s__Polaromonas sp018780625	77.4454	237	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002381615.1	s__Polaromonas sp002381615	77.3061	223	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016000195.1	s__Polaromonas sp016000195	77.2553	243	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	98.70	98.70	0.94	0.94	2	-
GCA_004293655.1	s__Polaromonas sp004293655	77.192	174	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824015.1	s__Polaromonas sp013824015	77.1851	179	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012927415.1	s__Polaromonas sp012927415	77.1705	219	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012927445.1	s__Rhodoferax sp012927445	76.8827	161	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.76	98.76	0.94	0.94	2	-
GCA_903960915.1	s__Rhodoferax sp903960915	76.6181	147	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.23	97.99	0.89	0.81	4	-
GCA_903897925.1	s__Rhodoferax sp903897925	76.4557	128	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.65	99.65	0.87	0.87	2	-
GCA_903840825.1	s__Rhodoferax sp903840825	76.3176	97	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:20,352] [INFO] GTDB search result was written to GCF_012584515.1_ASM1258451v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:20,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:20,357] [INFO] DFAST_QC result json was written to GCF_012584515.1_ASM1258451v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:20,357] [INFO] DFAST_QC completed!
[2024-01-24 12:00:20,357] [INFO] Total running time: 0h1m24s