[2024-01-24 14:46:35,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg768ecd77-8460-4a60-930c-07f21f1ff2d5/dqc_reference
[2024-01-24 14:46:37,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:37,181] [INFO] Task started: Prodigal
[2024-01-24 14:46:37,181] [INFO] Running command: gunzip -c /var/lib/cwl/stg26fe6390-5393-49aa-a0de-13544580f2f5/GCF_001661675.2_ASM166167v2_genomic.fna.gz | prodigal -d GCF_001661675.2_ASM166167v2_genomic.fna/cds.fna -a GCF_001661675.2_ASM166167v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:49,264] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:49,264] [INFO] Task started: HMMsearch
[2024-01-24 14:46:49,264] [INFO] Running command: hmmsearch --tblout GCF_001661675.2_ASM166167v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg768ecd77-8460-4a60-930c-07f21f1ff2d5/dqc_reference/reference_markers.hmm GCF_001661675.2_ASM166167v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:49,461] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:49,463] [INFO] Found 6/6 markers.
[2024-01-24 14:46:49,498] [INFO] Query marker FASTA was written to GCF_001661675.2_ASM166167v2_genomic.fna/markers.fasta
[2024-01-24 14:46:49,499] [INFO] Task started: Blastn
[2024-01-24 14:46:49,499] [INFO] Running command: blastn -query GCF_001661675.2_ASM166167v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg768ecd77-8460-4a60-930c-07f21f1ff2d5/dqc_reference/reference_markers.fasta -out GCF_001661675.2_ASM166167v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:50,340] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:50,343] [INFO] Selected 16 target genomes.
[2024-01-24 14:46:50,344] [INFO] Target genome list was writen to GCF_001661675.2_ASM166167v2_genomic.fna/target_genomes.txt
[2024-01-24 14:46:50,350] [INFO] Task started: fastANI
[2024-01-24 14:46:50,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg26fe6390-5393-49aa-a0de-13544580f2f5/GCF_001661675.2_ASM166167v2_genomic.fna.gz --refList GCF_001661675.2_ASM166167v2_genomic.fna/target_genomes.txt --output GCF_001661675.2_ASM166167v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:01,834] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:01,834] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg768ecd77-8460-4a60-930c-07f21f1ff2d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:01,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg768ecd77-8460-4a60-930c-07f21f1ff2d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:01,847] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:01,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:01,847] [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
Croceicoccus marinus	strain=E4A9	GCA_001661675.2	450378	450378	type	True	100.0	1366	1368	95	conclusive
Croceicoccus mobilis	strain=Ery22	GCA_001661965.1	1703339	1703339	type	True	82.8995	715	1368	95	below_threshold
Croceicoccus mobilis	strain=CGMCC 1.15360	GCA_014642595.1	1703339	1703339	type	True	82.8061	727	1368	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	80.8136	513	1368	95	below_threshold
Croceicoccus bisphenolivorans	strain=H4	GCA_001634625.1	1783232	1783232	type	True	80.3926	502	1368	95	below_threshold
Croceicoccus naphthovorans	strain=PQ-2	GCA_001028705.1	1348774	1348774	type	True	80.2833	507	1368	95	below_threshold
Croceicoccus naphthovorans	strain=DSM 102796	GCA_014196855.1	1348774	1348774	type	True	80.2123	499	1368	95	below_threshold
Croceicoccus gelatinilyticus	strain=1NDH52	GCA_018398395.1	2835536	2835536	type	True	80.0455	530	1368	95	below_threshold
Croceicoccus pelagius	strain=Ery9	GCA_001661915.1	1703341	1703341	type	True	79.994	507	1368	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	79.7951	523	1368	95	below_threshold
Croceicoccus ponticola	strain=GM-16	GCA_004004515.1	2217664	2217664	type	True	79.3314	446	1368	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.8884	369	1368	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.741	352	1368	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.7194	380	1368	95	below_threshold
Novosphingobium pokkalii	strain=KCTC 42224	GCA_014652855.1	1770194	1770194	type	True	78.4214	424	1368	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	78.0078	320	1368	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:01,849] [INFO] DFAST Taxonomy check result was written to GCF_001661675.2_ASM166167v2_genomic.fna/tc_result.tsv
[2024-01-24 14:47:01,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:01,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:01,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg768ecd77-8460-4a60-930c-07f21f1ff2d5/dqc_reference/checkm_data
[2024-01-24 14:47:01,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:01,888] [INFO] Task started: CheckM
[2024-01-24 14:47:01,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001661675.2_ASM166167v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001661675.2_ASM166167v2_genomic.fna/checkm_input GCF_001661675.2_ASM166167v2_genomic.fna/checkm_result
[2024-01-24 14:47:38,057] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:38,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:38,079] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:38,079] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:38,079] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001661675.2_ASM166167v2_genomic.fna/markers.fasta)
[2024-01-24 14:47:38,080] [INFO] Task started: Blastn
[2024-01-24 14:47:38,080] [INFO] Running command: blastn -query GCF_001661675.2_ASM166167v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg768ecd77-8460-4a60-930c-07f21f1ff2d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_001661675.2_ASM166167v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:39,517] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:39,520] [INFO] Selected 12 target genomes.
[2024-01-24 14:47:39,521] [INFO] Target genome list was writen to GCF_001661675.2_ASM166167v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:39,529] [INFO] Task started: fastANI
[2024-01-24 14:47:39,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg26fe6390-5393-49aa-a0de-13544580f2f5/GCF_001661675.2_ASM166167v2_genomic.fna.gz --refList GCF_001661675.2_ASM166167v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001661675.2_ASM166167v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:49,485] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:49,496] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:49,496] [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_001661675.2	s__Croceicoccus marinus	100.0	1367	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	96.65	96.65	0.86	0.86	2	conclusive
GCA_002694745.1	s__Croceicoccus sp002694745	88.1774	929	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	99.91	99.91	0.91	0.91	2	-
GCF_001661965.1	s__Croceicoccus mobilis	82.946	711	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001028705.1	s__Croceicoccus naphthovorans	80.266	509	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018398395.1	s__Croceicoccus sp018398395	80.0298	532	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661915.1	s__Croceicoccus pelagius	79.9494	507	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007570835.1	s__Croceicoccus sediminis	79.7951	523	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745095.1	s__Croceicoccus sp016745095	79.6057	496	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004004515.1	s__Croceicoccus ponticola	79.3355	446	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	78.6244	450	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652855.1	s__Novosphingobium pokkalii	78.4395	422	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745295.1	s__Novosphingobium sp017745295	78.1485	395	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:47:49,497] [INFO] GTDB search result was written to GCF_001661675.2_ASM166167v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:49,498] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:49,501] [INFO] DFAST_QC result json was written to GCF_001661675.2_ASM166167v2_genomic.fna/dqc_result.json
[2024-01-24 14:47:49,502] [INFO] DFAST_QC completed!
[2024-01-24 14:47:49,502] [INFO] Total running time: 0h1m14s