[2023-06-27 15:00:48,468] [INFO] DFAST_QC pipeline started.
[2023-06-27 15:00:48,472] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 15:00:48,473] [INFO] DQC Reference Directory: /var/lib/cwl/stg61b7dad9-4e68-496d-ab10-7f4df0b8f29e/dqc_reference
[2023-06-27 15:00:49,794] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 15:00:49,795] [INFO] Task started: Prodigal
[2023-06-27 15:00:49,795] [INFO] Running command: gunzip -c /var/lib/cwl/stg287a389f-909e-49d9-94f5-2b283c4d883b/GCA_002281915.1_ASM228191v1_genomic.fna.gz | prodigal -d GCA_002281915.1_ASM228191v1_genomic.fna/cds.fna -a GCA_002281915.1_ASM228191v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 15:01:02,667] [INFO] Task succeeded: Prodigal
[2023-06-27 15:01:02,667] [INFO] Task started: HMMsearch
[2023-06-27 15:01:02,668] [INFO] Running command: hmmsearch --tblout GCA_002281915.1_ASM228191v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61b7dad9-4e68-496d-ab10-7f4df0b8f29e/dqc_reference/reference_markers.hmm GCA_002281915.1_ASM228191v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 15:01:02,918] [INFO] Task succeeded: HMMsearch
[2023-06-27 15:01:02,920] [INFO] Found 6/6 markers.
[2023-06-27 15:01:02,949] [INFO] Query marker FASTA was written to GCA_002281915.1_ASM228191v1_genomic.fna/markers.fasta
[2023-06-27 15:01:02,950] [INFO] Task started: Blastn
[2023-06-27 15:01:02,950] [INFO] Running command: blastn -query GCA_002281915.1_ASM228191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b7dad9-4e68-496d-ab10-7f4df0b8f29e/dqc_reference/reference_markers.fasta -out GCA_002281915.1_ASM228191v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:01:03,693] [INFO] Task succeeded: Blastn
[2023-06-27 15:01:03,699] [INFO] Selected 27 target genomes.
[2023-06-27 15:01:03,699] [INFO] Target genome list was writen to GCA_002281915.1_ASM228191v1_genomic.fna/target_genomes.txt
[2023-06-27 15:01:03,704] [INFO] Task started: fastANI
[2023-06-27 15:01:03,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg287a389f-909e-49d9-94f5-2b283c4d883b/GCA_002281915.1_ASM228191v1_genomic.fna.gz --refList GCA_002281915.1_ASM228191v1_genomic.fna/target_genomes.txt --output GCA_002281915.1_ASM228191v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 15:01:21,342] [INFO] Task succeeded: fastANI
[2023-06-27 15:01:21,343] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61b7dad9-4e68-496d-ab10-7f4df0b8f29e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 15:01:21,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61b7dad9-4e68-496d-ab10-7f4df0b8f29e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 15:01:21,367] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 15:01:21,367] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 15:01:21,367] [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
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	86.9428	614	862	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	79.5651	326	862	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	78.9912	302	862	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	78.8772	303	862	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	77.7722	217	862	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	77.7233	200	862	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	77.6869	229	862	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	77.6711	220	862	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	77.5707	228	862	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	77.5645	243	862	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	77.5366	200	862	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	77.5247	231	862	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	77.3632	188	862	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	77.3132	166	862	95	below_threshold
Comamonas kerstersii	strain=CCUG 15333	GCA_008801935.1	225992	225992	type	True	77.2133	188	862	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	77.1366	207	862	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	77.1048	155	862	95	below_threshold
Diaphorobacter ruginosibacter	strain=DSM 27467	GCA_014395975.1	1715720	1715720	type	True	76.9448	164	862	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	76.809	193	862	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	76.7141	174	862	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	76.6876	133	862	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	76.686	135	862	95	below_threshold
Inhella inkyongensis	strain=IMCC1713	GCA_005952805.1	392593	392593	type	True	76.2152	105	862	95	below_threshold
Inhella inkyongensis	strain=DSM 23958	GCA_014202795.1	392593	392593	type	True	76.1916	105	862	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 15:01:21,370] [INFO] DFAST Taxonomy check result was written to GCA_002281915.1_ASM228191v1_genomic.fna/tc_result.tsv
[2023-06-27 15:01:21,371] [INFO] ===== Taxonomy check completed =====
[2023-06-27 15:01:21,371] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 15:01:21,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61b7dad9-4e68-496d-ab10-7f4df0b8f29e/dqc_reference/checkm_data
[2023-06-27 15:01:21,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 15:01:21,402] [INFO] Task started: CheckM
[2023-06-27 15:01:21,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002281915.1_ASM228191v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002281915.1_ASM228191v1_genomic.fna/checkm_input GCA_002281915.1_ASM228191v1_genomic.fna/checkm_result
[2023-06-27 15:02:02,773] [INFO] Task succeeded: CheckM
[2023-06-27 15:02:02,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 15:02:02,806] [INFO] ===== Completeness check finished =====
[2023-06-27 15:02:02,807] [INFO] ===== Start GTDB Search =====
[2023-06-27 15:02:02,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002281915.1_ASM228191v1_genomic.fna/markers.fasta)
[2023-06-27 15:02:02,808] [INFO] Task started: Blastn
[2023-06-27 15:02:02,808] [INFO] Running command: blastn -query GCA_002281915.1_ASM228191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b7dad9-4e68-496d-ab10-7f4df0b8f29e/dqc_reference/reference_markers_gtdb.fasta -out GCA_002281915.1_ASM228191v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:02:04,159] [INFO] Task succeeded: Blastn
[2023-06-27 15:02:04,164] [INFO] Selected 7 target genomes.
[2023-06-27 15:02:04,165] [INFO] Target genome list was writen to GCA_002281915.1_ASM228191v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 15:02:04,170] [INFO] Task started: fastANI
[2023-06-27 15:02:04,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg287a389f-909e-49d9-94f5-2b283c4d883b/GCA_002281915.1_ASM228191v1_genomic.fna.gz --refList GCA_002281915.1_ASM228191v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002281915.1_ASM228191v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 15:02:08,751] [INFO] Task succeeded: fastANI
[2023-06-27 15:02:08,762] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 15:02:08,762] [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_002282445.1	s__Limnohabitans sp002282445	99.9975	839	862	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	100.00	100.00	0.99	0.99	3	conclusive
GCF_003063545.1	s__Limnohabitans sp003063545	88.9122	596	862	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063475.1	s__Limnohabitans curvus	86.9587	613	862	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.49	98.49	0.87	0.87	2	-
GCA_903952885.1	s__Limnohabitans sp903952885	85.4579	400	862	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.13	99.13	0.83	0.83	2	-
GCA_903886485.1	s__Limnohabitans sp903886485	84.6227	558	862	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.98	99.98	0.98	0.98	3	-
GCF_002778325.1	s__Limnohabitans sp002778325	83.0207	543	862	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002778315.1	s__Limnohabitans sp002778315	80.4385	481	862	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.08	98.08	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-27 15:02:08,764] [INFO] GTDB search result was written to GCA_002281915.1_ASM228191v1_genomic.fna/result_gtdb.tsv
[2023-06-27 15:02:08,765] [INFO] ===== GTDB Search completed =====
[2023-06-27 15:02:08,770] [INFO] DFAST_QC result json was written to GCA_002281915.1_ASM228191v1_genomic.fna/dqc_result.json
[2023-06-27 15:02:08,770] [INFO] DFAST_QC completed!
[2023-06-27 15:02:08,770] [INFO] Total running time: 0h1m20s