[2024-01-25 18:49:50,920] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:50,923] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:50,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg09d08900-efae-4304-8446-56632cb6ee24/dqc_reference
[2024-01-25 18:49:52,086] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:52,087] [INFO] Task started: Prodigal
[2024-01-25 18:49:52,087] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4128688-d9fb-40a7-96db-64781d96398f/GCF_025567165.1_ASM2556716v1_genomic.fna.gz | prodigal -d GCF_025567165.1_ASM2556716v1_genomic.fna/cds.fna -a GCF_025567165.1_ASM2556716v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:59,822] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:59,822] [INFO] Task started: HMMsearch
[2024-01-25 18:49:59,822] [INFO] Running command: hmmsearch --tblout GCF_025567165.1_ASM2556716v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09d08900-efae-4304-8446-56632cb6ee24/dqc_reference/reference_markers.hmm GCF_025567165.1_ASM2556716v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:00,052] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:00,053] [INFO] Found 6/6 markers.
[2024-01-25 18:50:00,086] [INFO] Query marker FASTA was written to GCF_025567165.1_ASM2556716v1_genomic.fna/markers.fasta
[2024-01-25 18:50:00,087] [INFO] Task started: Blastn
[2024-01-25 18:50:00,087] [INFO] Running command: blastn -query GCF_025567165.1_ASM2556716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09d08900-efae-4304-8446-56632cb6ee24/dqc_reference/reference_markers.fasta -out GCF_025567165.1_ASM2556716v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:00,694] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:00,697] [INFO] Selected 24 target genomes.
[2024-01-25 18:50:00,697] [INFO] Target genome list was writen to GCF_025567165.1_ASM2556716v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:00,723] [INFO] Task started: fastANI
[2024-01-25 18:50:00,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4128688-d9fb-40a7-96db-64781d96398f/GCF_025567165.1_ASM2556716v1_genomic.fna.gz --refList GCF_025567165.1_ASM2556716v1_genomic.fna/target_genomes.txt --output GCF_025567165.1_ASM2556716v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:17,153] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:17,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09d08900-efae-4304-8446-56632cb6ee24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:17,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09d08900-efae-4304-8446-56632cb6ee24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:17,166] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:50:17,166] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:50:17,166] [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
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	84.2645	80	1158	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	83.9655	79	1158	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	80.8744	76	1158	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	80.8218	101	1158	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.3324	73	1158	95	below_threshold
Bariatricus massiliensis	strain=AT12	GCA_900086725.1	1745713	1745713	type	True	79.2612	57	1158	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	79.261	92	1158	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	78.9765	104	1158	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	78.6125	133	1158	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	78.5372	63	1158	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	78.3471	91	1158	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	78.1613	70	1158	95	below_threshold
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	77.838	77	1158	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	77.7323	79	1158	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	77.7019	83	1158	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	77.5258	90	1158	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	77.4943	90	1158	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.4715	99	1158	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	77.3934	92	1158	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	77.3069	73	1158	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.8514	119	1158	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.8025	118	1158	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:17,168] [INFO] DFAST Taxonomy check result was written to GCF_025567165.1_ASM2556716v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:17,168] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:17,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:17,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09d08900-efae-4304-8446-56632cb6ee24/dqc_reference/checkm_data
[2024-01-25 18:50:17,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:17,205] [INFO] Task started: CheckM
[2024-01-25 18:50:17,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567165.1_ASM2556716v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567165.1_ASM2556716v1_genomic.fna/checkm_input GCF_025567165.1_ASM2556716v1_genomic.fna/checkm_result
[2024-01-25 18:50:43,768] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:43,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:43,789] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:43,789] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:43,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567165.1_ASM2556716v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:43,790] [INFO] Task started: Blastn
[2024-01-25 18:50:43,790] [INFO] Running command: blastn -query GCF_025567165.1_ASM2556716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09d08900-efae-4304-8446-56632cb6ee24/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567165.1_ASM2556716v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:44,926] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:44,929] [INFO] Selected 14 target genomes.
[2024-01-25 18:50:44,929] [INFO] Target genome list was writen to GCF_025567165.1_ASM2556716v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:44,949] [INFO] Task started: fastANI
[2024-01-25 18:50:44,949] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4128688-d9fb-40a7-96db-64781d96398f/GCF_025567165.1_ASM2556716v1_genomic.fna.gz --refList GCF_025567165.1_ASM2556716v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567165.1_ASM2556716v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:55,595] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:55,605] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:50:55,605] [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_902362725.1	s__Merdisoma sp900066385	100.0	1155	1158	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	98.97	97.93	0.91	0.83	3	conclusive
GCA_900553635.1	s__Merdisoma sp900553635	90.5063	510	1158	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	97.48	97.13	0.82	0.78	3	-
GCF_014290175.1	s__Merdisoma sp014290175	86.738	700	1158	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.98	99.96	0.81	0.62	3	-
GCA_018223435.1	s__Limivivens sp900543575	80.2628	169	1158	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.02	97.88	0.92	0.90	4	-
GCF_002160825.1	s__Merdisoma sp002160825	79.3412	336	1158	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.04	99.04	0.92	0.92	2	-
GCF_002160765.1	s__Merdisoma faecalis	79.1482	371	1158	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	98.59	98.32	0.91	0.81	8	-
GCF_900086725.1	s__Bariatricus massiliensis	79.1143	59	1158	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.97	99.97	0.99	0.99	2	-
GCA_910576325.1	s__Merdisoma sp910576325	78.3964	257	1158	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	100.00	99.99	1.00	1.00	6	-
GCA_018715645.1	s__Merdisoma merdipullorum	78.3846	274	1158	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.92	99.92	0.91	0.91	2	-
GCA_910575725.1	s__Merdisoma sp011959465	78.3052	254	1158	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.24	98.50	0.89	0.80	3	-
GCA_910574835.1	s__Merdisoma sp910574835	78.2842	221	1158	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586955.1	s__Merdisoma sp910586955	77.2269	203	1158	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:55,607] [INFO] GTDB search result was written to GCF_025567165.1_ASM2556716v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:55,607] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:55,611] [INFO] DFAST_QC result json was written to GCF_025567165.1_ASM2556716v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:55,611] [INFO] DFAST_QC completed!
[2024-01-25 18:50:55,611] [INFO] Total running time: 0h1m5s