[2023-06-27 05:57:40,850] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:57:40,852] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:57:40,853] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fc947f2-cb63-4050-a4cf-581b169d524b/dqc_reference
[2023-06-27 05:57:42,185] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:57:42,186] [INFO] Task started: Prodigal
[2023-06-27 05:57:42,186] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe85e56d-6950-4989-9575-0a7346db8436/GCA_026224775.1_ASM2622477v1_genomic.fna.gz | prodigal -d GCA_026224775.1_ASM2622477v1_genomic.fna/cds.fna -a GCA_026224775.1_ASM2622477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:58:03,458] [INFO] Task succeeded: Prodigal
[2023-06-27 05:58:03,458] [INFO] Task started: HMMsearch
[2023-06-27 05:58:03,458] [INFO] Running command: hmmsearch --tblout GCA_026224775.1_ASM2622477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fc947f2-cb63-4050-a4cf-581b169d524b/dqc_reference/reference_markers.hmm GCA_026224775.1_ASM2622477v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:58:03,808] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:58:03,809] [INFO] Found 6/6 markers.
[2023-06-27 05:58:03,857] [INFO] Query marker FASTA was written to GCA_026224775.1_ASM2622477v1_genomic.fna/markers.fasta
[2023-06-27 05:58:03,857] [INFO] Task started: Blastn
[2023-06-27 05:58:03,857] [INFO] Running command: blastn -query GCA_026224775.1_ASM2622477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fc947f2-cb63-4050-a4cf-581b169d524b/dqc_reference/reference_markers.fasta -out GCA_026224775.1_ASM2622477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:58:04,475] [INFO] Task succeeded: Blastn
[2023-06-27 05:58:04,480] [INFO] Selected 18 target genomes.
[2023-06-27 05:58:04,481] [INFO] Target genome list was writen to GCA_026224775.1_ASM2622477v1_genomic.fna/target_genomes.txt
[2023-06-27 05:58:04,482] [INFO] Task started: fastANI
[2023-06-27 05:58:04,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe85e56d-6950-4989-9575-0a7346db8436/GCA_026224775.1_ASM2622477v1_genomic.fna.gz --refList GCA_026224775.1_ASM2622477v1_genomic.fna/target_genomes.txt --output GCA_026224775.1_ASM2622477v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:58:22,596] [INFO] Task succeeded: fastANI
[2023-06-27 05:58:22,597] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fc947f2-cb63-4050-a4cf-581b169d524b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:58:22,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fc947f2-cb63-4050-a4cf-581b169d524b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:58:22,614] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:58:22,614] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 05:58:22,615] [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
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	79.6589	698	1779	95	below_threshold
Mucilaginibacter frigoritolerans	strain=ATCC BAA-1854	GCA_007830615.1	652788	652788	type	True	77.8648	367	1779	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.4919	353	1779	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.4807	279	1779	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	77.4084	346	1779	95	below_threshold
Mucilaginibacter lappiensis	strain=ANJLi2	GCA_014200545.1	354630	354630	type	True	77.4049	346	1779	95	below_threshold
Mucilaginibacter inviolabilis	strain=HC2	GCA_011089895.1	2714892	2714892	type	True	77.3997	334	1779	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	77.3593	312	1779	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.3579	253	1779	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.3265	212	1779	95	below_threshold
Mucilaginibacter gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	77.3041	311	1779	95	below_threshold
Mucilaginibacter xinganensis	strain=BJC16-A31	GCA_002257585.1	1234841	1234841	type	True	77.2362	306	1779	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	77.1908	236	1779	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.1883	255	1779	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.0032	218	1779	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.0019	232	1779	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:58:22,617] [INFO] DFAST Taxonomy check result was written to GCA_026224775.1_ASM2622477v1_genomic.fna/tc_result.tsv
[2023-06-27 05:58:22,617] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:58:22,617] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:58:22,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fc947f2-cb63-4050-a4cf-581b169d524b/dqc_reference/checkm_data
[2023-06-27 05:58:22,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:58:22,674] [INFO] Task started: CheckM
[2023-06-27 05:58:22,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026224775.1_ASM2622477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026224775.1_ASM2622477v1_genomic.fna/checkm_input GCA_026224775.1_ASM2622477v1_genomic.fna/checkm_result
[2023-06-27 05:59:23,005] [INFO] Task succeeded: CheckM
[2023-06-27 05:59:23,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.02%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 05:59:23,032] [INFO] ===== Completeness check finished =====
[2023-06-27 05:59:23,032] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:59:23,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026224775.1_ASM2622477v1_genomic.fna/markers.fasta)
[2023-06-27 05:59:23,033] [INFO] Task started: Blastn
[2023-06-27 05:59:23,033] [INFO] Running command: blastn -query GCA_026224775.1_ASM2622477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fc947f2-cb63-4050-a4cf-581b169d524b/dqc_reference/reference_markers_gtdb.fasta -out GCA_026224775.1_ASM2622477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:59:23,806] [INFO] Task succeeded: Blastn
[2023-06-27 05:59:23,812] [INFO] Selected 10 target genomes.
[2023-06-27 05:59:23,812] [INFO] Target genome list was writen to GCA_026224775.1_ASM2622477v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:59:23,820] [INFO] Task started: fastANI
[2023-06-27 05:59:23,821] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe85e56d-6950-4989-9575-0a7346db8436/GCA_026224775.1_ASM2622477v1_genomic.fna.gz --refList GCA_026224775.1_ASM2622477v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026224775.1_ASM2622477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:59:35,326] [INFO] Task succeeded: fastANI
[2023-06-27 05:59:35,339] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 05:59:35,340] [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_009765905.1	s__Mucilaginibacter sp009765905	91.3651	1310	1779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013287375.1	s__Mucilaginibacter sp013287375	90.0226	749	1779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.48	99.44	0.60	0.60	3	-
GCF_013408825.1	s__Mucilaginibacter sp013408825	86.6458	1090	1779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200495.1	s__Mucilaginibacter sp014200495	79.8767	723	1779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105165.1	s__Mucilaginibacter mallensis	79.6368	700	1779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903915155.1	s__Mucilaginibacter sp903915155	78.6808	450	1779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403905.1	s__Mucilaginibacter sp002403905	77.5303	266	1779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.52	99.50	0.82	0.82	3	-
GCF_900101875.1	s__Mucilaginibacter pineti	77.5266	349	1779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155965.1	s__Mucilaginibacter lappiensis	77.3999	347	1779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.12	98.24	0.94	0.88	3	-
GCF_002257585.1	s__Mucilaginibacter xinganensis	77.2362	306	1779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 05:59:35,368] [INFO] GTDB search result was written to GCA_026224775.1_ASM2622477v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:59:35,368] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:59:35,383] [INFO] DFAST_QC result json was written to GCA_026224775.1_ASM2622477v1_genomic.fna/dqc_result.json
[2023-06-27 05:59:35,383] [INFO] DFAST_QC completed!
[2023-06-27 05:59:35,383] [INFO] Total running time: 0h1m55s