[2024-01-24 13:09:47,768] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:47,770] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:47,770] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f4e5aec-59e7-4821-ab3f-330ba5153dc4/dqc_reference
[2024-01-24 13:09:49,033] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:49,034] [INFO] Task started: Prodigal
[2024-01-24 13:09:49,034] [INFO] Running command: gunzip -c /var/lib/cwl/stg00e252ac-8b90-4c50-a408-118953d5798d/GCF_003432115.1_ASM343211v1_genomic.fna.gz | prodigal -d GCF_003432115.1_ASM343211v1_genomic.fna/cds.fna -a GCF_003432115.1_ASM343211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:13,443] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:13,443] [INFO] Task started: HMMsearch
[2024-01-24 13:10:13,444] [INFO] Running command: hmmsearch --tblout GCF_003432115.1_ASM343211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f4e5aec-59e7-4821-ab3f-330ba5153dc4/dqc_reference/reference_markers.hmm GCF_003432115.1_ASM343211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:13,816] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:13,818] [INFO] Found 6/6 markers.
[2024-01-24 13:10:13,879] [INFO] Query marker FASTA was written to GCF_003432115.1_ASM343211v1_genomic.fna/markers.fasta
[2024-01-24 13:10:13,879] [INFO] Task started: Blastn
[2024-01-24 13:10:13,879] [INFO] Running command: blastn -query GCF_003432115.1_ASM343211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f4e5aec-59e7-4821-ab3f-330ba5153dc4/dqc_reference/reference_markers.fasta -out GCF_003432115.1_ASM343211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:14,484] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:14,487] [INFO] Selected 14 target genomes.
[2024-01-24 13:10:14,488] [INFO] Target genome list was writen to GCF_003432115.1_ASM343211v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:14,495] [INFO] Task started: fastANI
[2024-01-24 13:10:14,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg00e252ac-8b90-4c50-a408-118953d5798d/GCF_003432115.1_ASM343211v1_genomic.fna.gz --refList GCF_003432115.1_ASM343211v1_genomic.fna/target_genomes.txt --output GCF_003432115.1_ASM343211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:29,015] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:29,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f4e5aec-59e7-4821-ab3f-330ba5153dc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:29,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f4e5aec-59e7-4821-ab3f-330ba5153dc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:29,027] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:29,028] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:29,028] [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 conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	100.0	1771	1772	95	conclusive
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	82.2643	907	1772	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	78.923	620	1772	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	78.892	636	1772	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	78.8505	663	1772	95	below_threshold
Mucilaginibacter pedocola	strain=TBZ30	GCA_002013915.1	1792845	1792845	type	True	78.7944	633	1772	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	78.6229	505	1772	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	78.2347	495	1772	95	below_threshold
Mucilaginibacter psychrotolerans	strain=NH7-4	GCA_004519315.1	1524096	1524096	type	True	78.0134	477	1772	95	below_threshold
Mucilaginibacter corticis	strain=MAH-19	GCA_007558865.1	2597670	2597670	type	True	77.487	330	1772	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	77.439	410	1772	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.3646	285	1772	95	below_threshold
Mucilaginibacter xinganensis	strain=BJC16-A31	GCA_002257585.1	1234841	1234841	type	True	77.3215	253	1772	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:29,029] [INFO] DFAST Taxonomy check result was written to GCF_003432115.1_ASM343211v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:29,030] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:29,030] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:29,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f4e5aec-59e7-4821-ab3f-330ba5153dc4/dqc_reference/checkm_data
[2024-01-24 13:10:29,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:29,082] [INFO] Task started: CheckM
[2024-01-24 13:10:29,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003432115.1_ASM343211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003432115.1_ASM343211v1_genomic.fna/checkm_input GCF_003432115.1_ASM343211v1_genomic.fna/checkm_result
[2024-01-24 13:11:35,443] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:35,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:35,467] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:35,468] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:35,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003432115.1_ASM343211v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:35,469] [INFO] Task started: Blastn
[2024-01-24 13:11:35,469] [INFO] Running command: blastn -query GCF_003432115.1_ASM343211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f4e5aec-59e7-4821-ab3f-330ba5153dc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003432115.1_ASM343211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:36,242] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:36,245] [INFO] Selected 9 target genomes.
[2024-01-24 13:11:36,246] [INFO] Target genome list was writen to GCF_003432115.1_ASM343211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:36,253] [INFO] Task started: fastANI
[2024-01-24 13:11:36,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg00e252ac-8b90-4c50-a408-118953d5798d/GCF_003432115.1_ASM343211v1_genomic.fna.gz --refList GCF_003432115.1_ASM343211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003432115.1_ASM343211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:46,466] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:46,478] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:46,478] [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_003432115.1	s__Mucilaginibacter sp003432115	100.0	1771	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016763755.1	s__Mucilaginibacter sp016763755	84.8838	1021	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007846095.1	s__Mucilaginibacter sp007846095	82.2653	907	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288635.1	s__Mucilaginibacter sp002288635	80.7418	720	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898335.1	s__Mucilaginibacter sp001898335	80.7417	705	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.32	99.30	0.92	0.89	3	-
GCF_004168255.1	s__Mucilaginibacter terrigena	78.8534	662	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002013915.1	s__Mucilaginibacter pedocola	78.7881	634	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007558865.1	s__Mucilaginibacter corticis	77.4875	330	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149275.1	s__Mucilaginibacter sp013149275	77.4422	370	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:46,493] [INFO] GTDB search result was written to GCF_003432115.1_ASM343211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:46,494] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:46,499] [INFO] DFAST_QC result json was written to GCF_003432115.1_ASM343211v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:46,499] [INFO] DFAST_QC completed!
[2024-01-24 13:11:46,499] [INFO] Total running time: 0h1m59s