[2024-01-25 19:38:20,596] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:20,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:20,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg32c9209a-e722-4dd8-a16a-1a0dd3f23cc8/dqc_reference
[2024-01-25 19:38:21,788] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:21,789] [INFO] Task started: Prodigal
[2024-01-25 19:38:21,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg919b53a0-f31d-44d5-a85f-5ab4d8b8b1fa/GCF_003073145.1_ASM307314v1_genomic.fna.gz | prodigal -d GCF_003073145.1_ASM307314v1_genomic.fna/cds.fna -a GCF_003073145.1_ASM307314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:34,955] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:34,956] [INFO] Task started: HMMsearch
[2024-01-25 19:38:34,956] [INFO] Running command: hmmsearch --tblout GCF_003073145.1_ASM307314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32c9209a-e722-4dd8-a16a-1a0dd3f23cc8/dqc_reference/reference_markers.hmm GCF_003073145.1_ASM307314v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:35,236] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:35,239] [INFO] Found 6/6 markers.
[2024-01-25 19:38:35,290] [INFO] Query marker FASTA was written to GCF_003073145.1_ASM307314v1_genomic.fna/markers.fasta
[2024-01-25 19:38:35,290] [INFO] Task started: Blastn
[2024-01-25 19:38:35,291] [INFO] Running command: blastn -query GCF_003073145.1_ASM307314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32c9209a-e722-4dd8-a16a-1a0dd3f23cc8/dqc_reference/reference_markers.fasta -out GCF_003073145.1_ASM307314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:36,274] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:36,277] [INFO] Selected 11 target genomes.
[2024-01-25 19:38:36,277] [INFO] Target genome list was writen to GCF_003073145.1_ASM307314v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:36,286] [INFO] Task started: fastANI
[2024-01-25 19:38:36,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg919b53a0-f31d-44d5-a85f-5ab4d8b8b1fa/GCF_003073145.1_ASM307314v1_genomic.fna.gz --refList GCF_003073145.1_ASM307314v1_genomic.fna/target_genomes.txt --output GCF_003073145.1_ASM307314v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:38:48,459] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:48,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32c9209a-e722-4dd8-a16a-1a0dd3f23cc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:38:48,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32c9209a-e722-4dd8-a16a-1a0dd3f23cc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:38:48,467] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:38:48,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:38:48,468] [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
Acuticoccus yangtzensis	strain=JL1095	GCA_003073145.1	1443441	1443441	type	True	100.0	1677	1679	95	conclusive
Acuticoccus yangtzensis	strain=JL1095	GCA_001927245.1	1443441	1443441	type	True	99.9982	1661	1679	95	conclusive
Acuticoccus sediminis	strain=PTG4-2	GCA_003258595.1	2184697	2184697	type	True	82.5428	1203	1679	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	79.5145	730	1679	95	below_threshold
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	79.3451	790	1679	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	77.054	263	1679	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.4681	347	1679	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	76.4206	437	1679	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.3377	354	1679	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	75.827	203	1679	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	75.49	116	1679	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:38:48,469] [INFO] DFAST Taxonomy check result was written to GCF_003073145.1_ASM307314v1_genomic.fna/tc_result.tsv
[2024-01-25 19:38:48,470] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:38:48,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:38:48,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32c9209a-e722-4dd8-a16a-1a0dd3f23cc8/dqc_reference/checkm_data
[2024-01-25 19:38:48,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:38:48,534] [INFO] Task started: CheckM
[2024-01-25 19:38:48,534] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003073145.1_ASM307314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003073145.1_ASM307314v1_genomic.fna/checkm_input GCF_003073145.1_ASM307314v1_genomic.fna/checkm_result
[2024-01-25 19:39:33,523] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:33,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:33,546] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:33,546] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:33,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003073145.1_ASM307314v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:33,546] [INFO] Task started: Blastn
[2024-01-25 19:39:33,546] [INFO] Running command: blastn -query GCF_003073145.1_ASM307314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32c9209a-e722-4dd8-a16a-1a0dd3f23cc8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003073145.1_ASM307314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:35,418] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:35,429] [INFO] Selected 18 target genomes.
[2024-01-25 19:39:35,429] [INFO] Target genome list was writen to GCF_003073145.1_ASM307314v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:35,448] [INFO] Task started: fastANI
[2024-01-25 19:39:35,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg919b53a0-f31d-44d5-a85f-5ab4d8b8b1fa/GCF_003073145.1_ASM307314v1_genomic.fna.gz --refList GCF_003073145.1_ASM307314v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003073145.1_ASM307314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:52,445] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:52,456] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:52,457] [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_001927245.1	s__Acuticoccus yangtzensis	99.9982	1661	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	98.76	97.53	0.97	0.95	3	conclusive
GCF_003258595.1	s__Acuticoccus sediminis	82.5352	1203	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016411865.1	s__Acuticoccus sp016411865	79.4604	739	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374525.1	s__Amorphus coralli	77.2834	369	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Amorphus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789575.1	s__Stappia indica_A	77.0151	385	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	76.9152	448	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_002844595.1	s__Pleomorphomonas diazotrophica	76.8978	206	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004297465.1	s__SCUB01 sp004297465	76.798	225	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__SCUB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009600605.1	s__Pseudoxanthobacter spirostomi	76.7748	403	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425185.1	s__Pleomorphomonas koreensis	76.7516	310	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	95.03	95.03	0.88	0.88	2	-
GCA_002722295.1	s__Stappia sp002722295	76.6934	264	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	99.88	99.88	0.88	0.88	2	-
GCF_012275355.1	s__Xanthobacter sp012275355	76.5945	344	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004004555.2	s__Methylobacterium sp004004555	76.5094	428	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013044135.1	s__Enterovirga sp013044135	76.4809	243	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Enterovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013377085.1	s__Rhodoplanes sp013377085	76.2492	342	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820275.1	s__Brevundimonas sp018820275	75.9368	188	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCF_014641735.1	s__Sphingomonas metalli	75.82	204	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992075.1	s__Pararhodospirillum oryzae	75.49	116	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:52,458] [INFO] GTDB search result was written to GCF_003073145.1_ASM307314v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:52,459] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:52,462] [INFO] DFAST_QC result json was written to GCF_003073145.1_ASM307314v1_genomic.fna/dqc_result.json
[2024-01-25 19:39:52,462] [INFO] DFAST_QC completed!
[2024-01-25 19:39:52,462] [INFO] Total running time: 0h1m32s