[2024-01-25 18:03:20,414] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:20,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:20,416] [INFO] DQC Reference Directory: /var/lib/cwl/stgce304a15-3018-4389-a5e4-1ead60ac1bd6/dqc_reference
[2024-01-25 18:03:21,523] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:21,524] [INFO] Task started: Prodigal
[2024-01-25 18:03:21,524] [INFO] Running command: gunzip -c /var/lib/cwl/stg21b014c0-c742-40b9-be19-f12d87eab790/GCF_024436435.1_ASM2443643v1_genomic.fna.gz | prodigal -d GCF_024436435.1_ASM2443643v1_genomic.fna/cds.fna -a GCF_024436435.1_ASM2443643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:39,606] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:39,606] [INFO] Task started: HMMsearch
[2024-01-25 18:03:39,606] [INFO] Running command: hmmsearch --tblout GCF_024436435.1_ASM2443643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce304a15-3018-4389-a5e4-1ead60ac1bd6/dqc_reference/reference_markers.hmm GCF_024436435.1_ASM2443643v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:39,925] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:39,928] [INFO] Found 6/6 markers.
[2024-01-25 18:03:39,972] [INFO] Query marker FASTA was written to GCF_024436435.1_ASM2443643v1_genomic.fna/markers.fasta
[2024-01-25 18:03:39,972] [INFO] Task started: Blastn
[2024-01-25 18:03:39,973] [INFO] Running command: blastn -query GCF_024436435.1_ASM2443643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce304a15-3018-4389-a5e4-1ead60ac1bd6/dqc_reference/reference_markers.fasta -out GCF_024436435.1_ASM2443643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:40,554] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:40,557] [INFO] Selected 20 target genomes.
[2024-01-25 18:03:40,557] [INFO] Target genome list was writen to GCF_024436435.1_ASM2443643v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:40,593] [INFO] Task started: fastANI
[2024-01-25 18:03:40,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg21b014c0-c742-40b9-be19-f12d87eab790/GCF_024436435.1_ASM2443643v1_genomic.fna.gz --refList GCF_024436435.1_ASM2443643v1_genomic.fna/target_genomes.txt --output GCF_024436435.1_ASM2443643v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:58,831] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:58,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce304a15-3018-4389-a5e4-1ead60ac1bd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:58,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce304a15-3018-4389-a5e4-1ead60ac1bd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:58,841] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:58,841] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:58,841] [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
Pedobacter xinjiangensis	strain=CCTCC AB 208092	GCA_024436435.1	539206	539206	type	True	100.0	1823	1825	95	conclusive
Pedobacter mongoliensis	strain=KCTC 52859	GCA_024436395.1	2100740	2100740	type	True	77.6366	123	1825	95	below_threshold
Flavihumibacter soli	strain=R14	GCA_010692725.1	2705549	2705549	type	True	77.4669	57	1825	95	below_threshold
Daejeonella rubra	strain=DSM 24536	GCA_900103545.1	990371	990371	type	True	77.0088	63	1825	95	below_threshold
Pararcticibacter amylolyticus	strain=FJ4-8	GCA_003130405.1	2173175	2173175	type	True	76.9248	119	1825	95	below_threshold
Arcticibacter tournemirensis	strain=DSM 23085	GCA_006716645.1	699437	699437	type	True	76.8837	118	1825	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	76.8225	52	1825	95	below_threshold
Arcticibacter tournemirensis	strain=TF5-37.2-LB10	GCA_008690275.1	699437	699437	type	True	76.8016	117	1825	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	76.6921	55	1825	95	below_threshold
Arcticibacter svalbardensis	strain=MN12-7	GCA_000403135.1	1288027	1288027	type	True	76.6777	93	1825	95	below_threshold
Pedobacter hartonius	strain=DSM 19033	GCA_900107535.1	425514	425514	type	True	76.6082	52	1825	95	below_threshold
Pedobacter insulae	strain=DSM 18684	GCA_900113525.1	414048	414048	type	True	76.4802	50	1825	95	below_threshold
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	76.3878	59	1825	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	76.2	64	1825	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:58,843] [INFO] DFAST Taxonomy check result was written to GCF_024436435.1_ASM2443643v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:58,843] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:58,843] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:58,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce304a15-3018-4389-a5e4-1ead60ac1bd6/dqc_reference/checkm_data
[2024-01-25 18:03:58,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:58,895] [INFO] Task started: CheckM
[2024-01-25 18:03:58,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024436435.1_ASM2443643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024436435.1_ASM2443643v1_genomic.fna/checkm_input GCF_024436435.1_ASM2443643v1_genomic.fna/checkm_result
[2024-01-25 18:04:51,110] [INFO] Task succeeded: CheckM
[2024-01-25 18:04:51,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:04:51,141] [INFO] ===== Completeness check finished =====
[2024-01-25 18:04:51,141] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:04:51,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024436435.1_ASM2443643v1_genomic.fna/markers.fasta)
[2024-01-25 18:04:51,143] [INFO] Task started: Blastn
[2024-01-25 18:04:51,143] [INFO] Running command: blastn -query GCF_024436435.1_ASM2443643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce304a15-3018-4389-a5e4-1ead60ac1bd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_024436435.1_ASM2443643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:52,064] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:52,071] [INFO] Selected 25 target genomes.
[2024-01-25 18:04:52,071] [INFO] Target genome list was writen to GCF_024436435.1_ASM2443643v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:04:52,087] [INFO] Task started: fastANI
[2024-01-25 18:04:52,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg21b014c0-c742-40b9-be19-f12d87eab790/GCF_024436435.1_ASM2443643v1_genomic.fna.gz --refList GCF_024436435.1_ASM2443643v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024436435.1_ASM2443643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:16,789] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:16,800] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:05:16,801] [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_017355835.1	s__SYSU-D00535 sp017355835	78.3475	198	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355855.1	s__SYSU-D00535 sp017355855	77.9639	171	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355785.1	s__SYSU-D00535 sp017355785	77.9525	200	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834875.1	s__HMF7647 sp009834875	77.4818	72	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__HMF7647	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010692725.1	s__Daejeonella soli	77.4669	57	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018492665.1	s__Pedobacter sp018492665	77.107	51	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103545.1	s__Daejeonella rubra	77.0088	63	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130405.1	s__Pararcticibacter amylolyticus	76.9441	117	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716645.1	s__Pararcticibacter tournemirensis	76.8865	119	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	98.22	96.45	0.92	0.83	3	-
GCA_014380615.1	s__JACMJM01 sp014380615	76.8801	112	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__JACMJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223055.1	s__Pedobacter sp015223055	76.798	65	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403135.1	s__Arcticibacter svalbardensis	76.6777	93	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Arcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107535.1	s__Pedobacter hartonius	76.6082	52	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765905.1	s__Mucilaginibacter sp009765905	76.5846	59	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113525.1	s__Pedobacter insulae	76.4802	50	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576455.2	s__Mucilaginibacter celer	76.4488	64	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258495.1	s__Pedobacter agri	76.3878	59	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.48	97.42	0.86	0.85	3	-
GCF_900110105.1	s__Mucilaginibacter gossypiicola	76.2087	65	1825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:16,802] [INFO] GTDB search result was written to GCF_024436435.1_ASM2443643v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:16,802] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:16,806] [INFO] DFAST_QC result json was written to GCF_024436435.1_ASM2443643v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:16,806] [INFO] DFAST_QC completed!
[2024-01-25 18:05:16,806] [INFO] Total running time: 0h1m56s