[2023-06-08 07:02:26,413] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:02:26,420] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:02:26,421] [INFO] DQC Reference Directory: /var/lib/cwl/stg0795464e-d318-4d49-8081-785feb9eaeb4/dqc_reference
[2023-06-08 07:02:27,941] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:02:27,942] [INFO] Task started: Prodigal
[2023-06-08 07:02:27,942] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d50412e-7afc-415a-8251-4c3117e07099/GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna.gz | prodigal -d GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/cds.fna -a GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:02:35,844] [INFO] Task succeeded: Prodigal
[2023-06-08 07:02:35,845] [INFO] Task started: HMMsearch
[2023-06-08 07:02:35,845] [INFO] Running command: hmmsearch --tblout GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0795464e-d318-4d49-8081-785feb9eaeb4/dqc_reference/reference_markers.hmm GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:02:36,135] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:02:36,137] [INFO] Found 6/6 markers.
[2023-06-08 07:02:36,171] [INFO] Query marker FASTA was written to GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/markers.fasta
[2023-06-08 07:02:36,172] [INFO] Task started: Blastn
[2023-06-08 07:02:36,172] [INFO] Running command: blastn -query GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/markers.fasta -db /var/lib/cwl/stg0795464e-d318-4d49-8081-785feb9eaeb4/dqc_reference/reference_markers.fasta -out GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:02:36,874] [INFO] Task succeeded: Blastn
[2023-06-08 07:02:36,883] [INFO] Selected 31 target genomes.
[2023-06-08 07:02:36,884] [INFO] Target genome list was writen to GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/target_genomes.txt
[2023-06-08 07:02:36,887] [INFO] Task started: fastANI
[2023-06-08 07:02:36,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d50412e-7afc-415a-8251-4c3117e07099/GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna.gz --refList GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/target_genomes.txt --output GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:02:55,717] [INFO] Task succeeded: fastANI
[2023-06-08 07:02:55,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0795464e-d318-4d49-8081-785feb9eaeb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:02:55,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0795464e-d318-4d49-8081-785feb9eaeb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:02:55,734] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:02:55,734] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 07:02:55,734] [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
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.9326	88	1036	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	77.5898	74	1036	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.581	60	1036	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	77.4476	64	1036	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	77.3729	89	1036	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	77.2128	93	1036	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	77.0751	97	1036	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	76.937	72	1036	95	below_threshold
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	76.9039	50	1036	95	below_threshold
Jutongia huaianensis	strain=NSJ-37	GCA_014384985.1	2763668	2763668	type	True	76.8306	55	1036	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.648	79	1036	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	76.6473	79	1036	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	76.552	61	1036	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	76.5058	62	1036	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	76.4974	55	1036	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	76.4791	64	1036	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	76.0207	64	1036	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 07:02:55,738] [INFO] DFAST Taxonomy check result was written to GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/tc_result.tsv
[2023-06-08 07:02:55,738] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:02:55,739] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:02:55,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0795464e-d318-4d49-8081-785feb9eaeb4/dqc_reference/checkm_data
[2023-06-08 07:02:55,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:02:55,777] [INFO] Task started: CheckM
[2023-06-08 07:02:55,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/checkm_input GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/checkm_result
[2023-06-08 07:03:24,799] [INFO] Task succeeded: CheckM
[2023-06-08 07:03:24,801] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:03:24,824] [INFO] ===== Completeness check finished =====
[2023-06-08 07:03:24,824] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:03:24,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/markers.fasta)
[2023-06-08 07:03:24,825] [INFO] Task started: Blastn
[2023-06-08 07:03:24,825] [INFO] Running command: blastn -query GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/markers.fasta -db /var/lib/cwl/stg0795464e-d318-4d49-8081-785feb9eaeb4/dqc_reference/reference_markers_gtdb.fasta -out GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:03:25,916] [INFO] Task succeeded: Blastn
[2023-06-08 07:03:25,921] [INFO] Selected 20 target genomes.
[2023-06-08 07:03:25,921] [INFO] Target genome list was writen to GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:03:25,926] [INFO] Task started: fastANI
[2023-06-08 07:03:25,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d50412e-7afc-415a-8251-4c3117e07099/GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna.gz --refList GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/target_genomes_gtdb.txt --output GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:03:36,621] [INFO] Task succeeded: fastANI
[2023-06-08 07:03:36,641] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 07:03:36,641] [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_900553305.1	s__CAG-95 sp900553305	93.0671	581	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.81	99.81	0.85	0.85	2	-
GCA_000438155.1	s__CAG-95 sp000438155	92.8218	765	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.06	97.32	0.83	0.81	5	-
GCA_003490145.1	s__CAG-95 sp900066375	78.5822	222	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.74	97.55	0.91	0.82	5	-
GCA_000436115.1	s__CAG-95 sp000436115	78.1083	208	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.37	99.32	0.91	0.90	3	-
GCA_017434885.1	s__CAG-95 sp017434885	77.9717	159	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766365.1	s__CAG-95 sp902766365	77.9548	196	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017411305.1	s__CAG-95 sp017411305	77.734	145	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900772845.1	s__Acetatifactor sp900772845	77.6438	123	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	95.92	95.92	0.80	0.80	2	-
GCA_009774465.1	s__CAG-95 sp009774465	77.4488	124	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.09	98.09	0.83	0.83	2	-
GCA_018384375.1	s__CAG-95 sp018384375	77.4385	197	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.73	98.22	0.80	0.77	3	-
GCA_017622575.1	s__CAG-95 sp017622575	77.4276	192	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804285.1	s__CAG-95 sp014804285	77.3767	120	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000403495.2	s__CAG-95 sp000403495	77.2229	126	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.68	98.68	0.87	0.87	2	-
GCA_910585005.1	s__CAG-95 sp910585005	77.139	113	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621815.1	s__CAG-95 sp017621815	76.9783	156	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002431915.1	s__Acetatifactor sp002431915	76.8761	114	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900755865.1	s__Acetatifactor sp900755865	76.8267	80	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.03	98.03	0.82	0.82	2	-
GCA_017461865.1	s__CAG-194 sp017461865	76.5349	51	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-194	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017467845.1	s__Acetatifactor sp017467845	76.4591	76	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621115.1	s__RGIG8767 sp017621115	76.4476	50	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG8767	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 07:03:36,643] [INFO] GTDB search result was written to GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/result_gtdb.tsv
[2023-06-08 07:03:36,643] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:03:36,648] [INFO] DFAST_QC result json was written to GCA_902461415.1_UHGG-TPA_MGYG-HGUT-00325_genomic.fna/dqc_result.json
[2023-06-08 07:03:36,648] [INFO] DFAST_QC completed!
[2023-06-08 07:03:36,648] [INFO] Total running time: 0h1m10s