[2023-06-30 05:30:24,177] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:30:24,179] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:30:24,180] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a70f877-ba7d-4163-b855-c806a094dac4/dqc_reference
[2023-06-30 05:30:25,476] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:30:25,477] [INFO] Task started: Prodigal
[2023-06-30 05:30:25,477] [INFO] Running command: gunzip -c /var/lib/cwl/stg13c3d492-cd52-47b4-885c-2c6ac5e4fce8/GCA_016764475.1_ASM1676447v1_genomic.fna.gz | prodigal -d GCA_016764475.1_ASM1676447v1_genomic.fna/cds.fna -a GCA_016764475.1_ASM1676447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:30:34,217] [INFO] Task succeeded: Prodigal
[2023-06-30 05:30:34,218] [INFO] Task started: HMMsearch
[2023-06-30 05:30:34,218] [INFO] Running command: hmmsearch --tblout GCA_016764475.1_ASM1676447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a70f877-ba7d-4163-b855-c806a094dac4/dqc_reference/reference_markers.hmm GCA_016764475.1_ASM1676447v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:30:34,487] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:30:34,488] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg13c3d492-cd52-47b4-885c-2c6ac5e4fce8/GCA_016764475.1_ASM1676447v1_genomic.fna.gz]
[2023-06-30 05:30:34,516] [INFO] Query marker FASTA was written to GCA_016764475.1_ASM1676447v1_genomic.fna/markers.fasta
[2023-06-30 05:30:34,517] [INFO] Task started: Blastn
[2023-06-30 05:30:34,517] [INFO] Running command: blastn -query GCA_016764475.1_ASM1676447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a70f877-ba7d-4163-b855-c806a094dac4/dqc_reference/reference_markers.fasta -out GCA_016764475.1_ASM1676447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:30:35,273] [INFO] Task succeeded: Blastn
[2023-06-30 05:30:35,276] [INFO] Selected 27 target genomes.
[2023-06-30 05:30:35,277] [INFO] Target genome list was writen to GCA_016764475.1_ASM1676447v1_genomic.fna/target_genomes.txt
[2023-06-30 05:30:35,278] [INFO] Task started: fastANI
[2023-06-30 05:30:35,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg13c3d492-cd52-47b4-885c-2c6ac5e4fce8/GCA_016764475.1_ASM1676447v1_genomic.fna.gz --refList GCA_016764475.1_ASM1676447v1_genomic.fna/target_genomes.txt --output GCA_016764475.1_ASM1676447v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:30:51,753] [INFO] Task succeeded: fastANI
[2023-06-30 05:30:51,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a70f877-ba7d-4163-b855-c806a094dac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:30:51,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a70f877-ba7d-4163-b855-c806a094dac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:30:51,773] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:30:51,773] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 05:30:51,773] [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
Amylibacter kogurei	strain=4G11	GCA_002742285.1	1889778	1889778	type	True	76.7261	124	944	95	below_threshold
Amylibacter ulvae	strain=KCTC 32465	GCA_014652655.1	1651968	1651968	type	True	76.6003	120	944	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	76.1619	58	944	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.1619	58	944	95	below_threshold
Thalassococcus halodurans	strain=DSM 26915	GCA_900108225.1	373675	373675	type	True	76.0515	56	944	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	75.9975	56	944	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	75.9668	51	944	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	75.9566	59	944	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	75.8474	73	944	95	below_threshold
Roseinatronobacter thiooxidans	strain=DSM 13087	GCA_003254005.1	121821	121821	type	True	75.8351	54	944	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	75.829	74	944	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	75.7868	59	944	95	below_threshold
Roseinatronobacter thiooxidans	strain=ALG1	GCA_001870675.1	121821	121821	type	True	75.777	55	944	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.713	52	944	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	75.6889	71	944	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 05:30:51,776] [INFO] DFAST Taxonomy check result was written to GCA_016764475.1_ASM1676447v1_genomic.fna/tc_result.tsv
[2023-06-30 05:30:51,776] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:30:51,776] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:30:51,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a70f877-ba7d-4163-b855-c806a094dac4/dqc_reference/checkm_data
[2023-06-30 05:30:51,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:30:51,809] [INFO] Task started: CheckM
[2023-06-30 05:30:51,809] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016764475.1_ASM1676447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016764475.1_ASM1676447v1_genomic.fna/checkm_input GCA_016764475.1_ASM1676447v1_genomic.fna/checkm_result
[2023-06-30 05:31:22,950] [INFO] Task succeeded: CheckM
[2023-06-30 05:31:22,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 12.88%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-30 05:31:22,974] [INFO] ===== Completeness check finished =====
[2023-06-30 05:31:22,975] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:31:22,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016764475.1_ASM1676447v1_genomic.fna/markers.fasta)
[2023-06-30 05:31:22,975] [INFO] Task started: Blastn
[2023-06-30 05:31:22,975] [INFO] Running command: blastn -query GCA_016764475.1_ASM1676447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a70f877-ba7d-4163-b855-c806a094dac4/dqc_reference/reference_markers_gtdb.fasta -out GCA_016764475.1_ASM1676447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:31:24,113] [INFO] Task succeeded: Blastn
[2023-06-30 05:31:24,119] [INFO] Selected 18 target genomes.
[2023-06-30 05:31:24,119] [INFO] Target genome list was writen to GCA_016764475.1_ASM1676447v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:31:24,136] [INFO] Task started: fastANI
[2023-06-30 05:31:24,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg13c3d492-cd52-47b4-885c-2c6ac5e4fce8/GCA_016764475.1_ASM1676447v1_genomic.fna.gz --refList GCA_016764475.1_ASM1676447v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016764475.1_ASM1676447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:31:34,097] [INFO] Task succeeded: fastANI
[2023-06-30 05:31:34,110] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 05:31:34,111] [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_016764475.1	s__Amylibacter sp016764475	100.0	937	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009184395.1	s__Amylibacter sp009184395	77.2816	176	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401045.1	s__Amylibacter sp002401045	77.1919	108	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090795.1	s__Amylibacter sp019090795	77.122	128	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162875.1	s__UBA3077 sp002162875	76.8746	50	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742285.1	s__Amylibacter kogurei	76.7434	123	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652655.1	s__Amylibacter ulvae	76.6171	119	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765235.1	s__UBA3077 sp016765235	76.5744	52	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223125.1	s__Amylibacter sp018223125	76.5121	120	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151535.1	s__UBA5972 sp013151535	76.3646	82	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643735.1	s__Amylibacter cionae	76.3595	115	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	75.9943	61	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	75.9712	85	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_900102535.1	s__Sulfitobacter delicatus	75.8222	59	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	75.7511	73	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-30 05:31:34,129] [INFO] GTDB search result was written to GCA_016764475.1_ASM1676447v1_genomic.fna/result_gtdb.tsv
[2023-06-30 05:31:34,130] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:31:34,136] [INFO] DFAST_QC result json was written to GCA_016764475.1_ASM1676447v1_genomic.fna/dqc_result.json
[2023-06-30 05:31:34,137] [INFO] DFAST_QC completed!
[2023-06-30 05:31:34,137] [INFO] Total running time: 0h1m10s