[2024-01-24 14:15:34,438] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:34,440] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:34,440] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7913292-f72a-4c9a-8179-c5dab09a97ad/dqc_reference
[2024-01-24 14:15:35,891] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,898] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,898] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d91671c-4bc6-4135-99ab-001a115b61bf/GCF_016522075.1_ASM1652207v1_genomic.fna.gz | prodigal -d GCF_016522075.1_ASM1652207v1_genomic.fna/cds.fna -a GCF_016522075.1_ASM1652207v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:52,458] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:52,458] [INFO] Task started: HMMsearch
[2024-01-24 14:15:52,458] [INFO] Running command: hmmsearch --tblout GCF_016522075.1_ASM1652207v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7913292-f72a-4c9a-8179-c5dab09a97ad/dqc_reference/reference_markers.hmm GCF_016522075.1_ASM1652207v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:52,815] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:52,817] [INFO] Found 6/6 markers.
[2024-01-24 14:15:52,861] [INFO] Query marker FASTA was written to GCF_016522075.1_ASM1652207v1_genomic.fna/markers.fasta
[2024-01-24 14:15:52,861] [INFO] Task started: Blastn
[2024-01-24 14:15:52,861] [INFO] Running command: blastn -query GCF_016522075.1_ASM1652207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7913292-f72a-4c9a-8179-c5dab09a97ad/dqc_reference/reference_markers.fasta -out GCF_016522075.1_ASM1652207v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:53,501] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:53,504] [INFO] Selected 25 target genomes.
[2024-01-24 14:15:53,505] [INFO] Target genome list was writen to GCF_016522075.1_ASM1652207v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:53,514] [INFO] Task started: fastANI
[2024-01-24 14:15:53,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d91671c-4bc6-4135-99ab-001a115b61bf/GCF_016522075.1_ASM1652207v1_genomic.fna.gz --refList GCF_016522075.1_ASM1652207v1_genomic.fna/target_genomes.txt --output GCF_016522075.1_ASM1652207v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:16,504] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:16,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7913292-f72a-4c9a-8179-c5dab09a97ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:16,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7913292-f72a-4c9a-8179-c5dab09a97ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:16,524] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:16:16,524] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:16:16,524] [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 segetis	strain=SD-g	GCA_016522075.1	2793071	2793071	type	True	100.0	1360	1360	95	conclusive
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	78.1293	401	1360	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	78.0882	396	1360	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	78.0854	402	1360	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	78.0766	405	1360	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	77.9109	346	1360	95	below_threshold
Mucilaginibacter pankratovii	strain=ZT4R22	GCA_014773265.1	2772110	2772110	type	True	77.8814	399	1360	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.8263	376	1360	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.625	301	1360	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.5273	323	1360	95	below_threshold
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	77.5087	247	1360	95	below_threshold
Mucilaginibacter terrenus	strain=ZH6	GCA_003432065.1	2482727	2482727	type	True	77.4945	260	1360	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.4942	295	1360	95	below_threshold
Mucilaginibacter lappiensis	strain=ANJLi2	GCA_014200545.1	354630	354630	type	True	77.4226	281	1360	95	below_threshold
Mucilaginibacter inviolabilis	strain=HC2	GCA_011089895.1	2714892	2714892	type	True	77.4175	312	1360	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	77.4116	254	1360	95	below_threshold
Mucilaginibacter corticis	strain=MAH-19	GCA_007558865.1	2597670	2597670	type	True	77.4059	229	1360	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	77.4015	284	1360	95	below_threshold
Mucilaginibacter gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	77.3813	253	1360	95	below_threshold
Mucilaginibacter kameinonensis	strain=SCK	GCA_003675385.1	452286	452286	type	True	77.3745	262	1360	95	below_threshold
Mucilaginibacter frigoritolerans	strain=ATCC BAA-1854	GCA_007830615.1	652788	652788	type	True	77.3016	255	1360	95	below_threshold
Mucilaginibacter robiniae	strain=F39-2	GCA_012849215.1	2728022	2728022	type	True	76.9627	116	1360	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	76.8401	51	1360	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	76.8052	179	1360	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	76.531	50	1360	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:16,526] [INFO] DFAST Taxonomy check result was written to GCF_016522075.1_ASM1652207v1_genomic.fna/tc_result.tsv
[2024-01-24 14:16:16,527] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:16,527] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:16,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7913292-f72a-4c9a-8179-c5dab09a97ad/dqc_reference/checkm_data
[2024-01-24 14:16:16,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:16,571] [INFO] Task started: CheckM
[2024-01-24 14:16:16,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016522075.1_ASM1652207v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016522075.1_ASM1652207v1_genomic.fna/checkm_input GCF_016522075.1_ASM1652207v1_genomic.fna/checkm_result
[2024-01-24 14:17:07,204] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:07,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:07,227] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:07,227] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:07,227] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016522075.1_ASM1652207v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:07,228] [INFO] Task started: Blastn
[2024-01-24 14:17:07,228] [INFO] Running command: blastn -query GCF_016522075.1_ASM1652207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7913292-f72a-4c9a-8179-c5dab09a97ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_016522075.1_ASM1652207v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:08,056] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:08,060] [INFO] Selected 22 target genomes.
[2024-01-24 14:17:08,060] [INFO] Target genome list was writen to GCF_016522075.1_ASM1652207v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:08,075] [INFO] Task started: fastANI
[2024-01-24 14:17:08,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d91671c-4bc6-4135-99ab-001a115b61bf/GCF_016522075.1_ASM1652207v1_genomic.fna.gz --refList GCF_016522075.1_ASM1652207v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016522075.1_ASM1652207v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:27,147] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:27,171] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:27,171] [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_016522075.1	s__Mucilaginibacter segetis	100.0	1360	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005938025.2	s__Mucilaginibacter sp005938025	78.4502	413	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093045.1	s__Mucilaginibacter sp010093045	78.2193	410	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.64	95.64	0.92	0.92	2	-
GCF_003635105.1	s__Mucilaginibacter sp003635105	78.2121	380	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636615.1	s__Mucilaginibacter sp001636615	78.176	401	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773275.1	s__Mucilaginibacter rigui	78.1092	416	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004378255.1	s__Mucilaginibacter phyllosphaerae	78.0882	396	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004168255.1	s__Mucilaginibacter terrigena	78.0682	406	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773265.1	s__Mucilaginibacter pankratovii	77.8814	399	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004054195.1	s__Mucilaginibacter sp004054195	77.8263	376	1360	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	77.5205	246	1360	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	77.5164	272	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101875.1	s__Mucilaginibacter pineti	77.4942	295	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200575.1	s__Mucilaginibacter sp014200575	77.4887	292	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011089895.1	s__Mucilaginibacter inviolabilis	77.4175	312	1360	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	77.4117	283	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.12	98.24	0.94	0.88	3	-
GCF_002355435.1	s__Mucilaginibacter gotjawali	77.3842	252	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_013286985.1	s__Mucilaginibacter sp013286985	77.3444	112	1360	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	77.1821	201	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.52	99.50	0.82	0.82	3	-
GCA_002413785.1	s__Mucilaginibacter sp002413785	77.0272	218	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.87	99.70	0.98	0.97	4	-
GCF_001705515.1	s__Mucilaginibacter sp001705515	76.9337	153	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799115.1	s__Pelobium glucosidilyticum_A	76.4865	56	1360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	97.72	97.72	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:27,173] [INFO] GTDB search result was written to GCF_016522075.1_ASM1652207v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:27,174] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:27,178] [INFO] DFAST_QC result json was written to GCF_016522075.1_ASM1652207v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:27,178] [INFO] DFAST_QC completed!
[2024-01-24 14:17:27,179] [INFO] Total running time: 0h1m53s