[2024-01-24 12:06:33,134] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,135] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,135] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bf21c54-b9cd-4052-95de-7d08a9a955fa/dqc_reference
[2024-01-24 12:06:34,308] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:34,309] [INFO] Task started: Prodigal
[2024-01-24 12:06:34,309] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d85604d-a120-49a1-99c4-b5d86cbd0c5f/GCF_003130405.1_ASM313040v1_genomic.fna.gz | prodigal -d GCF_003130405.1_ASM313040v1_genomic.fna/cds.fna -a GCF_003130405.1_ASM313040v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:59,675] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:59,676] [INFO] Task started: HMMsearch
[2024-01-24 12:06:59,676] [INFO] Running command: hmmsearch --tblout GCF_003130405.1_ASM313040v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bf21c54-b9cd-4052-95de-7d08a9a955fa/dqc_reference/reference_markers.hmm GCF_003130405.1_ASM313040v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:00,003] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:00,005] [INFO] Found 6/6 markers.
[2024-01-24 12:07:00,058] [INFO] Query marker FASTA was written to GCF_003130405.1_ASM313040v1_genomic.fna/markers.fasta
[2024-01-24 12:07:00,059] [INFO] Task started: Blastn
[2024-01-24 12:07:00,059] [INFO] Running command: blastn -query GCF_003130405.1_ASM313040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bf21c54-b9cd-4052-95de-7d08a9a955fa/dqc_reference/reference_markers.fasta -out GCF_003130405.1_ASM313040v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:00,668] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:00,672] [INFO] Selected 24 target genomes.
[2024-01-24 12:07:00,673] [INFO] Target genome list was writen to GCF_003130405.1_ASM313040v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:00,681] [INFO] Task started: fastANI
[2024-01-24 12:07:00,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d85604d-a120-49a1-99c4-b5d86cbd0c5f/GCF_003130405.1_ASM313040v1_genomic.fna.gz --refList GCF_003130405.1_ASM313040v1_genomic.fna/target_genomes.txt --output GCF_003130405.1_ASM313040v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:20,647] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:20,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bf21c54-b9cd-4052-95de-7d08a9a955fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:20,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bf21c54-b9cd-4052-95de-7d08a9a955fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:20,664] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:20,664] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:20,665] [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
Pararcticibacter amylolyticus	strain=FJ4-8	GCA_003130405.1	2173175	2173175	type	True	100.0	2052	2054	95	conclusive
Arcticibacter tournemirensis	strain=DSM 23085	GCA_006716645.1	699437	699437	type	True	78.8172	369	2054	95	below_threshold
Arcticibacter tournemirensis	strain=TF5-37.2-LB10	GCA_008690275.1	699437	699437	type	True	78.7945	368	2054	95	below_threshold
Arcticibacter pallidicorallinus	strain=CGMCC 1.9313	GCA_003002875.1	1259464	1259464	type	True	77.4328	118	2054	95	below_threshold
Pedobacter xinjiangensis	strain=CCTCC AB 208092	GCA_024436435.1	539206	539206	type	True	76.8297	129	2054	95	below_threshold
Pedobacter mongoliensis	strain=KCTC 52859	GCA_024436395.1	2100740	2100740	type	True	76.789	96	2054	95	below_threshold
Mucilaginibacter xinganensis	strain=BJC16-A31	GCA_002257585.1	1234841	1234841	type	True	76.5175	50	2054	95	below_threshold
Mucilaginibacter yixingensis	strain=DSM 26809	GCA_003050755.1	1295612	1295612	type	True	76.3358	58	2054	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	76.216	62	2054	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	76.0783	58	2054	95	below_threshold
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	75.9936	59	2054	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	75.9578	69	2054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:20,666] [INFO] DFAST Taxonomy check result was written to GCF_003130405.1_ASM313040v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:20,667] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:20,667] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:20,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bf21c54-b9cd-4052-95de-7d08a9a955fa/dqc_reference/checkm_data
[2024-01-24 12:07:20,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:20,726] [INFO] Task started: CheckM
[2024-01-24 12:07:20,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003130405.1_ASM313040v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003130405.1_ASM313040v1_genomic.fna/checkm_input GCF_003130405.1_ASM313040v1_genomic.fna/checkm_result
[2024-01-24 12:08:32,756] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:32,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:32,778] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:32,778] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:32,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003130405.1_ASM313040v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:32,779] [INFO] Task started: Blastn
[2024-01-24 12:08:32,779] [INFO] Running command: blastn -query GCF_003130405.1_ASM313040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bf21c54-b9cd-4052-95de-7d08a9a955fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_003130405.1_ASM313040v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:33,594] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:33,599] [INFO] Selected 26 target genomes.
[2024-01-24 12:08:33,599] [INFO] Target genome list was writen to GCF_003130405.1_ASM313040v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:33,638] [INFO] Task started: fastANI
[2024-01-24 12:08:33,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d85604d-a120-49a1-99c4-b5d86cbd0c5f/GCF_003130405.1_ASM313040v1_genomic.fna.gz --refList GCF_003130405.1_ASM313040v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003130405.1_ASM313040v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:55,908] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:55,921] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:55,922] [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_003130405.1	s__Pararcticibacter amylolyticus	100.0	2052	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006716645.1	s__Pararcticibacter tournemirensis	78.8177	368	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	98.22	96.45	0.92	0.83	3	-
GCF_003002875.1	s__Arcticibacter pallidicorallinus	77.4738	117	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Arcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355855.1	s__SYSU-D00535 sp017355855	77.4376	98	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654985.1	s__Pararcticibacter sp015654985	77.4067	264	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403135.1	s__Arcticibacter svalbardensis	77.2732	91	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Arcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834915.1	s__HMF7056 sp009834915	76.8447	60	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__HMF7056	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351025.1	s__Mucilaginibacter endophyticus	76.4952	65	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103545.1	s__Daejeonella rubra	76.3758	59	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100945.1	s__Mucilaginibacter gossypii	76.2544	62	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	96.19	95.83	0.85	0.84	10	-
GCF_014643835.1	s__Mucilaginibacter rubeus	76.126	56	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	97.62	97.51	0.93	0.92	3	-
GCF_900129215.1	s__Pedobacter caeni	76.0454	57	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103665.1	s__Pedobacter steynii	76.0009	67	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003852525.1	s__Pedobacter sp003852525	75.9334	67	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:55,925] [INFO] GTDB search result was written to GCF_003130405.1_ASM313040v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:55,925] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:55,929] [INFO] DFAST_QC result json was written to GCF_003130405.1_ASM313040v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:55,929] [INFO] DFAST_QC completed!
[2024-01-24 12:08:55,929] [INFO] Total running time: 0h2m23s