[2024-01-24 14:05:15,904] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:15,906] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:15,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a27d6cf-fe32-463b-aad6-f45f31d03865/dqc_reference
[2024-01-24 14:05:17,173] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:17,175] [INFO] Task started: Prodigal
[2024-01-24 14:05:17,175] [INFO] Running command: gunzip -c /var/lib/cwl/stg24a1e270-435a-4397-acb1-7a133225d122/GCF_019391655.1_ASM1939165v1_genomic.fna.gz | prodigal -d GCF_019391655.1_ASM1939165v1_genomic.fna/cds.fna -a GCF_019391655.1_ASM1939165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:37,079] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:37,079] [INFO] Task started: HMMsearch
[2024-01-24 14:05:37,080] [INFO] Running command: hmmsearch --tblout GCF_019391655.1_ASM1939165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a27d6cf-fe32-463b-aad6-f45f31d03865/dqc_reference/reference_markers.hmm GCF_019391655.1_ASM1939165v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:37,422] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:37,423] [INFO] Found 6/6 markers.
[2024-01-24 14:05:37,472] [INFO] Query marker FASTA was written to GCF_019391655.1_ASM1939165v1_genomic.fna/markers.fasta
[2024-01-24 14:05:37,472] [INFO] Task started: Blastn
[2024-01-24 14:05:37,472] [INFO] Running command: blastn -query GCF_019391655.1_ASM1939165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a27d6cf-fe32-463b-aad6-f45f31d03865/dqc_reference/reference_markers.fasta -out GCF_019391655.1_ASM1939165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:38,112] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:38,115] [INFO] Selected 25 target genomes.
[2024-01-24 14:05:38,116] [INFO] Target genome list was writen to GCF_019391655.1_ASM1939165v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:38,145] [INFO] Task started: fastANI
[2024-01-24 14:05:38,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg24a1e270-435a-4397-acb1-7a133225d122/GCF_019391655.1_ASM1939165v1_genomic.fna.gz --refList GCF_019391655.1_ASM1939165v1_genomic.fna/target_genomes.txt --output GCF_019391655.1_ASM1939165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:57,729] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:57,730] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a27d6cf-fe32-463b-aad6-f45f31d03865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:57,730] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a27d6cf-fe32-463b-aad6-f45f31d03865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:57,759] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:05:57,760] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:05:57,760] [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 gracilis	strain=DSM 18602	GCA_003633615.1	423350	423350	type	True	78.1442	419	1519	95	below_threshold
Mucilaginibacter paludis	strain=DSM 18603	GCA_000166195.3	423351	423351	type	True	77.9613	419	1519	95	below_threshold
Mucilaginibacter humi	strain=S1162	GCA_013087555.1	2732510	2732510	type	True	77.9552	121	1519	95	below_threshold
Mucilaginibacter polytrichastri	strain=RG4-7	GCA_001911425.1	1302689	1302689	type	True	77.6945	230	1519	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.6656	244	1519	95	below_threshold
Mucilaginibacter pankratovii	strain=ZT4R22	GCA_014773265.1	2772110	2772110	type	True	77.6581	273	1519	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.6444	186	1519	95	below_threshold
Mucilaginibacter polytrichastri	strain=DSM 26907	GCA_900116355.1	1302689	1302689	type	True	77.5716	224	1519	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.5675	246	1519	95	below_threshold
Mucilaginibacter corticis	strain=MAH-19	GCA_007558865.1	2597670	2597670	type	True	77.5351	249	1519	95	below_threshold
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	77.4726	250	1519	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.445	190	1519	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.4432	259	1519	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	77.4268	261	1519	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.4223	262	1519	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	77.4092	262	1519	95	below_threshold
Mucilaginibacter xinganensis	strain=BJC16-A31	GCA_002257585.1	1234841	1234841	type	True	77.4058	196	1519	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	77.3721	218	1519	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.3402	203	1519	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.3037	250	1519	95	below_threshold
Mucilaginibacter limnophilus	strain=YBJ-36	GCA_004005815.1	1932778	1932778	type	True	77.2193	182	1519	95	below_threshold
Mucilaginibacter auburnensis	strain=DSM 28175	GCA_002797815.1	1457233	1457233	type	True	77.1677	201	1519	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.0874	194	1519	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:57,762] [INFO] DFAST Taxonomy check result was written to GCF_019391655.1_ASM1939165v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:57,763] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:57,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:57,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a27d6cf-fe32-463b-aad6-f45f31d03865/dqc_reference/checkm_data
[2024-01-24 14:05:57,765] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:57,810] [INFO] Task started: CheckM
[2024-01-24 14:05:57,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019391655.1_ASM1939165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019391655.1_ASM1939165v1_genomic.fna/checkm_input GCF_019391655.1_ASM1939165v1_genomic.fna/checkm_result
[2024-01-24 14:06:53,928] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:53,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:53,952] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:53,952] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:53,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019391655.1_ASM1939165v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:53,953] [INFO] Task started: Blastn
[2024-01-24 14:06:53,953] [INFO] Running command: blastn -query GCF_019391655.1_ASM1939165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a27d6cf-fe32-463b-aad6-f45f31d03865/dqc_reference/reference_markers_gtdb.fasta -out GCF_019391655.1_ASM1939165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:54,780] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:54,784] [INFO] Selected 25 target genomes.
[2024-01-24 14:06:54,785] [INFO] Target genome list was writen to GCF_019391655.1_ASM1939165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:54,810] [INFO] Task started: fastANI
[2024-01-24 14:06:54,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg24a1e270-435a-4397-acb1-7a133225d122/GCF_019391655.1_ASM1939165v1_genomic.fna.gz --refList GCF_019391655.1_ASM1939165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019391655.1_ASM1939165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:18,916] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:18,949] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:07:18,949] [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
GCA_903893715.1	s__Mucilaginibacter sp903893715	79.2512	596	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.92	99.92	0.96	0.96	2	-
GCF_003633615.1	s__Mucilaginibacter gracilis	78.133	421	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001705515.1	s__Mucilaginibacter sp001705515	77.984	458	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166195.2	s__Mucilaginibacter paludis	77.9591	418	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001911425.1	s__Mucilaginibacter polytrichastri	77.681	231	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_014376655.1	s__Mucilaginibacter sp014376655	77.6207	170	1519	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	77.5788	245	1519	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	77.543	249	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168255.1	s__Mucilaginibacter terrigena	77.461	258	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257585.1	s__Mucilaginibacter xinganensis	77.4058	196	1519	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	77.3995	264	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCA_903915155.1	s__Mucilaginibacter sp903915155	77.3838	196	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288465.1	s__Mucilaginibacter sp013288465	77.3805	127	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408825.1	s__Mucilaginibacter sp013408825	77.3652	205	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765905.1	s__Mucilaginibacter sp009765905	77.3591	237	1519	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	77.3538	227	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.64	95.64	0.92	0.92	2	-
GCF_014200575.1	s__Mucilaginibacter sp014200575	77.3198	244	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223065.1	s__Mucilaginibacter sp015223065	77.2966	251	1519	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	77.2761	202	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.52	99.50	0.82	0.82	3	-
GCA_013286565.1	s__Mucilaginibacter sp013286565	77.1816	129	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797815.1	s__Mucilaginibacter auburnensis	77.1676	200	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390515.1	s__Mucilaginibacter sp018390515	77.1544	186	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675385.1	s__Mucilaginibacter kameinonensis	77.151	258	1519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.21	95.21	0.87	0.87	2	-
GCA_903644075.1	s__Mucilaginibacter sp903644075	77.0309	195	1519	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 14:07:18,951] [INFO] GTDB search result was written to GCF_019391655.1_ASM1939165v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:18,952] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:18,957] [INFO] DFAST_QC result json was written to GCF_019391655.1_ASM1939165v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:18,957] [INFO] DFAST_QC completed!
[2024-01-24 14:07:18,957] [INFO] Total running time: 0h2m3s