[2024-01-24 11:12:48,753] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:48,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:48,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg798083b7-2b00-45f2-b05f-bdd815f7aca2/dqc_reference
[2024-01-24 11:12:49,928] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:49,928] [INFO] Task started: Prodigal
[2024-01-24 11:12:49,929] [INFO] Running command: gunzip -c /var/lib/cwl/stg4601984e-b660-400b-b1d9-62e04d511ce5/GCF_016583825.1_ASM1658382v1_genomic.fna.gz | prodigal -d GCF_016583825.1_ASM1658382v1_genomic.fna/cds.fna -a GCF_016583825.1_ASM1658382v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:06,429] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:06,430] [INFO] Task started: HMMsearch
[2024-01-24 11:13:06,430] [INFO] Running command: hmmsearch --tblout GCF_016583825.1_ASM1658382v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg798083b7-2b00-45f2-b05f-bdd815f7aca2/dqc_reference/reference_markers.hmm GCF_016583825.1_ASM1658382v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:06,745] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:06,747] [INFO] Found 6/6 markers.
[2024-01-24 11:13:06,798] [INFO] Query marker FASTA was written to GCF_016583825.1_ASM1658382v1_genomic.fna/markers.fasta
[2024-01-24 11:13:06,799] [INFO] Task started: Blastn
[2024-01-24 11:13:06,799] [INFO] Running command: blastn -query GCF_016583825.1_ASM1658382v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg798083b7-2b00-45f2-b05f-bdd815f7aca2/dqc_reference/reference_markers.fasta -out GCF_016583825.1_ASM1658382v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:07,589] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:07,594] [INFO] Selected 23 target genomes.
[2024-01-24 11:13:07,594] [INFO] Target genome list was writen to GCF_016583825.1_ASM1658382v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:07,707] [INFO] Task started: fastANI
[2024-01-24 11:13:07,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg4601984e-b660-400b-b1d9-62e04d511ce5/GCF_016583825.1_ASM1658382v1_genomic.fna.gz --refList GCF_016583825.1_ASM1658382v1_genomic.fna/target_genomes.txt --output GCF_016583825.1_ASM1658382v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:25,514] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:25,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg798083b7-2b00-45f2-b05f-bdd815f7aca2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:25,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg798083b7-2b00-45f2-b05f-bdd815f7aca2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:25,533] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:25,534] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:25,534] [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
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	100.0	1774	1784	95	conclusive
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	79.5108	623	1784	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	78.751	576	1784	95	below_threshold
Halochromatium salexigens	strain=DSM 4395	GCA_016653295.1	49447	49447	type	True	78.503	478	1784	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	78.2511	432	1784	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	78.2211	435	1784	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	78.1992	422	1784	95	below_threshold
Halochromatium roseum	strain=DSM 18859	GCA_016653315.1	391920	391920	type	True	78.0955	425	1784	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	77.9607	330	1784	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	77.9158	357	1784	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	77.8481	387	1784	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	77.6546	356	1784	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	77.3893	334	1784	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	77.1645	291	1784	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.4272	211	1784	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	76.296	192	1784	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	76.2613	146	1784	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.1011	203	1784	95	below_threshold
Saccharospirillum salsuginis	strain=KCTC 22169	GCA_014651855.1	418750	418750	type	True	75.8087	70	1784	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	75.3754	88	1784	95	below_threshold
Actinomyces johnsonii	strain=CCUG 34287	GCA_006546835.1	544581	544581	type	True	75.0667	62	1784	95	below_threshold
Adlercreutzia muris	strain=DSM 29508	GCA_024623245.1	1796610	1796610	type	True	74.9467	51	1784	95	below_threshold
Adlercreutzia muris	strain=DSM 29508	GCA_008831045.1	1796610	1796610	type	True	74.9369	52	1784	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:25,537] [INFO] DFAST Taxonomy check result was written to GCF_016583825.1_ASM1658382v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:25,537] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:25,537] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:25,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg798083b7-2b00-45f2-b05f-bdd815f7aca2/dqc_reference/checkm_data
[2024-01-24 11:13:25,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:25,596] [INFO] Task started: CheckM
[2024-01-24 11:13:25,597] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583825.1_ASM1658382v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583825.1_ASM1658382v1_genomic.fna/checkm_input GCF_016583825.1_ASM1658382v1_genomic.fna/checkm_result
[2024-01-24 11:14:12,897] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:12,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:12,922] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:12,922] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:12,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583825.1_ASM1658382v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:12,923] [INFO] Task started: Blastn
[2024-01-24 11:14:12,923] [INFO] Running command: blastn -query GCF_016583825.1_ASM1658382v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg798083b7-2b00-45f2-b05f-bdd815f7aca2/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583825.1_ASM1658382v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:14,272] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:14,276] [INFO] Selected 17 target genomes.
[2024-01-24 11:14:14,276] [INFO] Target genome list was writen to GCF_016583825.1_ASM1658382v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:14,326] [INFO] Task started: fastANI
[2024-01-24 11:14:14,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg4601984e-b660-400b-b1d9-62e04d511ce5/GCF_016583825.1_ASM1658382v1_genomic.fna.gz --refList GCF_016583825.1_ASM1658382v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583825.1_ASM1658382v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:30,220] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:30,239] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:30,239] [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_016583825.1	s__Thiohalocapsa halophila	100.0	1774	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	95.31	95.31	0.87	0.87	2	conclusive
GCF_001469165.1	s__Thiohalocapsa sp001469165	81.66	1055	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008632335.1	s__Thiohalocapsa marina	79.5222	625	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584085.1	s__Halochromatium glycolicum	78.7508	576	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908845.1	s__Halochromatium sp009908845	78.6918	442	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653295.1	s__Halochromatium salexigens	78.515	476	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003562815.1	s__Halochromatium sp003562815	78.3248	362	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	99.58	99.39	0.91	0.88	4	-
GCF_018409545.1	s__Allochromatium tepidum	77.9276	328	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292295.1	s__Thiodictyon sp016292295	77.7025	195	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiodictyon	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693535.1	s__Halochromatium sp007693535	77.6698	428	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013385175.1	s__Allochromatium humboldtianum	77.6219	360	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720725.1	s__Allochromatium palmeri	77.5862	310	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938795.1	s__Marichromatium sp016938795	77.5117	222	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000228725.2	s__Thiorhodovibrio sp000228725	77.3994	301	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011392765.1	s__Thiosymbion ectosymbiont	77.0218	182	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiosymbion	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837595.1	s__Thiodictyon sp903837595	76.9529	330	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiodictyon	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651855.1	s__Saccharospirillum salsuginis	75.8087	70	1784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:30,241] [INFO] GTDB search result was written to GCF_016583825.1_ASM1658382v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:30,242] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:30,246] [INFO] DFAST_QC result json was written to GCF_016583825.1_ASM1658382v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:30,246] [INFO] DFAST_QC completed!
[2024-01-24 11:14:30,246] [INFO] Total running time: 0h1m41s