[2023-06-29 23:53:03,194] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:53:03,197] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:53:03,197] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bd6a0f6-e337-4fea-8bce-335154c419a0/dqc_reference
[2023-06-29 23:53:04,391] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:53:04,392] [INFO] Task started: Prodigal
[2023-06-29 23:53:04,393] [INFO] Running command: gunzip -c /var/lib/cwl/stge3b08551-37d6-4bba-be79-89f2535f66cd/GCA_019242385.1_ASM1924238v1_genomic.fna.gz | prodigal -d GCA_019242385.1_ASM1924238v1_genomic.fna/cds.fna -a GCA_019242385.1_ASM1924238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:53:09,903] [INFO] Task succeeded: Prodigal
[2023-06-29 23:53:09,904] [INFO] Task started: HMMsearch
[2023-06-29 23:53:09,904] [INFO] Running command: hmmsearch --tblout GCA_019242385.1_ASM1924238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bd6a0f6-e337-4fea-8bce-335154c419a0/dqc_reference/reference_markers.hmm GCA_019242385.1_ASM1924238v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:53:10,135] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:53:10,136] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge3b08551-37d6-4bba-be79-89f2535f66cd/GCA_019242385.1_ASM1924238v1_genomic.fna.gz]
[2023-06-29 23:53:10,159] [INFO] Query marker FASTA was written to GCA_019242385.1_ASM1924238v1_genomic.fna/markers.fasta
[2023-06-29 23:53:10,159] [INFO] Task started: Blastn
[2023-06-29 23:53:10,159] [INFO] Running command: blastn -query GCA_019242385.1_ASM1924238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bd6a0f6-e337-4fea-8bce-335154c419a0/dqc_reference/reference_markers.fasta -out GCA_019242385.1_ASM1924238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:53:10,965] [INFO] Task succeeded: Blastn
[2023-06-29 23:53:10,970] [INFO] Selected 30 target genomes.
[2023-06-29 23:53:10,971] [INFO] Target genome list was writen to GCA_019242385.1_ASM1924238v1_genomic.fna/target_genomes.txt
[2023-06-29 23:53:10,972] [INFO] Task started: fastANI
[2023-06-29 23:53:10,972] [INFO] Running command: fastANI --query /var/lib/cwl/stge3b08551-37d6-4bba-be79-89f2535f66cd/GCA_019242385.1_ASM1924238v1_genomic.fna.gz --refList GCA_019242385.1_ASM1924238v1_genomic.fna/target_genomes.txt --output GCA_019242385.1_ASM1924238v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:53:30,530] [INFO] Task succeeded: fastANI
[2023-06-29 23:53:30,531] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bd6a0f6-e337-4fea-8bce-335154c419a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:53:30,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bd6a0f6-e337-4fea-8bce-335154c419a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:53:30,551] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:53:30,552] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:53:30,552] [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
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	76.9254	69	557	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	76.8997	92	557	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	76.7256	87	557	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	76.5427	80	557	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	76.4425	77	557	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	76.4294	78	557	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	76.4276	73	557	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	76.2833	61	557	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.2242	73	557	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.1098	104	557	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.0814	61	557	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	76.0746	53	557	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.0397	61	557	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.0389	61	557	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	76.0206	52	557	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.836	56	557	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.7532	69	557	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	75.7475	72	557	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004799025.1	381431	381431	type	True	75.7072	54	557	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004364935.1	381431	381431	type	True	75.7058	54	557	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	75.4731	52	557	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	75.3495	77	557	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.1782	54	557	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:53:30,554] [INFO] DFAST Taxonomy check result was written to GCA_019242385.1_ASM1924238v1_genomic.fna/tc_result.tsv
[2023-06-29 23:53:30,555] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:53:30,555] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:53:30,555] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bd6a0f6-e337-4fea-8bce-335154c419a0/dqc_reference/checkm_data
[2023-06-29 23:53:30,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:53:30,584] [INFO] Task started: CheckM
[2023-06-29 23:53:30,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019242385.1_ASM1924238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019242385.1_ASM1924238v1_genomic.fna/checkm_input GCA_019242385.1_ASM1924238v1_genomic.fna/checkm_result
[2023-06-29 23:53:52,884] [INFO] Task succeeded: CheckM
[2023-06-29 23:53:52,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.04%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 23:53:52,911] [INFO] ===== Completeness check finished =====
[2023-06-29 23:53:52,911] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:53:52,912] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019242385.1_ASM1924238v1_genomic.fna/markers.fasta)
[2023-06-29 23:53:52,912] [INFO] Task started: Blastn
[2023-06-29 23:53:52,912] [INFO] Running command: blastn -query GCA_019242385.1_ASM1924238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bd6a0f6-e337-4fea-8bce-335154c419a0/dqc_reference/reference_markers_gtdb.fasta -out GCA_019242385.1_ASM1924238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:53:54,357] [INFO] Task succeeded: Blastn
[2023-06-29 23:53:54,362] [INFO] Selected 12 target genomes.
[2023-06-29 23:53:54,362] [INFO] Target genome list was writen to GCA_019242385.1_ASM1924238v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:53:54,366] [INFO] Task started: fastANI
[2023-06-29 23:53:54,366] [INFO] Running command: fastANI --query /var/lib/cwl/stge3b08551-37d6-4bba-be79-89f2535f66cd/GCA_019242385.1_ASM1924238v1_genomic.fna.gz --refList GCA_019242385.1_ASM1924238v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019242385.1_ASM1924238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:54:02,109] [INFO] Task succeeded: fastANI
[2023-06-29 23:54:02,124] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:54:02,124] [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_019242385.1	s__13-2-20CM-66-19 sp019242385	99.9999	546	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019235245.1	s__13-2-20CM-66-19 sp019235245	82.2984	399	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005878835.1	s__13-2-20CM-66-19 sp005878835	80.3124	351	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	98.03	96.96	0.89	0.85	6	-
GCA_005877965.1	s__13-2-20CM-66-19 sp005877965	80.0666	281	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240525.1	s__13-2-20CM-66-19 sp018240525	80.0106	312	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005878095.1	s__13-2-20CM-66-19 sp005878095	79.9702	343	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	99.52	99.52	0.84	0.84	2	-
GCA_001914695.1	s__13-2-20CM-66-19 sp001914695	79.9091	312	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	98.00	96.94	0.81	0.73	19	-
GCA_018241425.1	s__13-2-20CM-66-19 sp018241425	79.7832	325	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247195.1	s__13-2-20CM-66-19 sp019247195	79.2159	294	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	99.26	99.26	0.88	0.88	2	-
GCA_018241445.1	s__13-2-20CM-66-19 sp018241445	78.8974	262	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003156695.1	s__13-2-20CM-66-19 sp003156695	78.3304	221	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242685.1	s__ZC4RG24 sp003242685	78.1496	194	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG24	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:54:02,126] [INFO] GTDB search result was written to GCA_019242385.1_ASM1924238v1_genomic.fna/result_gtdb.tsv
[2023-06-29 23:54:02,127] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:54:02,130] [INFO] DFAST_QC result json was written to GCA_019242385.1_ASM1924238v1_genomic.fna/dqc_result.json
[2023-06-29 23:54:02,131] [INFO] DFAST_QC completed!
[2023-06-29 23:54:02,131] [INFO] Total running time: 0h0m59s