[2024-01-25 17:40:50,876] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:50,878] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:50,879] [INFO] DQC Reference Directory: /var/lib/cwl/stgd13d266b-4c67-4405-914b-ead206f09faa/dqc_reference
[2024-01-25 17:40:52,096] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:52,097] [INFO] Task started: Prodigal
[2024-01-25 17:40:52,097] [INFO] Running command: gunzip -c /var/lib/cwl/stga28077e7-1e7c-47cf-9ffc-7f182f6eb398/GCF_025567265.1_ASM2556726v1_genomic.fna.gz | prodigal -d GCF_025567265.1_ASM2556726v1_genomic.fna/cds.fna -a GCF_025567265.1_ASM2556726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:59,193] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:59,194] [INFO] Task started: HMMsearch
[2024-01-25 17:40:59,194] [INFO] Running command: hmmsearch --tblout GCF_025567265.1_ASM2556726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd13d266b-4c67-4405-914b-ead206f09faa/dqc_reference/reference_markers.hmm GCF_025567265.1_ASM2556726v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:59,418] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:59,419] [INFO] Found 6/6 markers.
[2024-01-25 17:40:59,448] [INFO] Query marker FASTA was written to GCF_025567265.1_ASM2556726v1_genomic.fna/markers.fasta
[2024-01-25 17:40:59,448] [INFO] Task started: Blastn
[2024-01-25 17:40:59,448] [INFO] Running command: blastn -query GCF_025567265.1_ASM2556726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd13d266b-4c67-4405-914b-ead206f09faa/dqc_reference/reference_markers.fasta -out GCF_025567265.1_ASM2556726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:00,054] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:00,057] [INFO] Selected 18 target genomes.
[2024-01-25 17:41:00,057] [INFO] Target genome list was writen to GCF_025567265.1_ASM2556726v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:00,074] [INFO] Task started: fastANI
[2024-01-25 17:41:00,074] [INFO] Running command: fastANI --query /var/lib/cwl/stga28077e7-1e7c-47cf-9ffc-7f182f6eb398/GCF_025567265.1_ASM2556726v1_genomic.fna.gz --refList GCF_025567265.1_ASM2556726v1_genomic.fna/target_genomes.txt --output GCF_025567265.1_ASM2556726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:11,256] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:11,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd13d266b-4c67-4405-914b-ead206f09faa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:11,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd13d266b-4c67-4405-914b-ead206f09faa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:11,267] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:41:11,267] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:41:11,268] [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
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	91.1481	719	1114	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	91.078	715	1114	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	82.075	295	1114	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	81.241	306	1114	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	81.18	305	1114	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	80.7687	182	1114	95	below_threshold
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	80.2989	59	1114	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	80.1811	198	1114	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.9931	189	1114	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	79.9416	212	1114	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	79.6955	186	1114	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	79.5903	182	1114	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	78.4617	64	1114	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	78.0144	139	1114	95	below_threshold
Konateibacter massiliensis	strain=Marseille-P3773	GCA_900184995.1	2002841	2002841	type	True	77.2637	51	1114	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.803	70	1114	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:11,269] [INFO] DFAST Taxonomy check result was written to GCF_025567265.1_ASM2556726v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:11,269] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:11,269] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:11,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd13d266b-4c67-4405-914b-ead206f09faa/dqc_reference/checkm_data
[2024-01-25 17:41:11,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:11,305] [INFO] Task started: CheckM
[2024-01-25 17:41:11,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567265.1_ASM2556726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567265.1_ASM2556726v1_genomic.fna/checkm_input GCF_025567265.1_ASM2556726v1_genomic.fna/checkm_result
[2024-01-25 17:41:37,745] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:37,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:37,775] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:37,775] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:37,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567265.1_ASM2556726v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:37,775] [INFO] Task started: Blastn
[2024-01-25 17:41:37,775] [INFO] Running command: blastn -query GCF_025567265.1_ASM2556726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd13d266b-4c67-4405-914b-ead206f09faa/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567265.1_ASM2556726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:38,820] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:38,824] [INFO] Selected 15 target genomes.
[2024-01-25 17:41:38,824] [INFO] Target genome list was writen to GCF_025567265.1_ASM2556726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:38,836] [INFO] Task started: fastANI
[2024-01-25 17:41:38,836] [INFO] Running command: fastANI --query /var/lib/cwl/stga28077e7-1e7c-47cf-9ffc-7f182f6eb398/GCF_025567265.1_ASM2556726v1_genomic.fna.gz --refList GCF_025567265.1_ASM2556726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567265.1_ASM2556726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:48,274] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:48,284] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:48,285] [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_001404875.1	s__Dorea_A longicatena_B	100.0	1111	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	97.75	96.72	0.80	0.69	20	conclusive
GCF_000154065.1	s__Dorea_A longicatena	91.1777	717	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	98.55	97.61	0.85	0.69	49	-
GCA_900550865.1	s__Dorea_A sp900550865	90.9594	591	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013300725.1	s__Bariatricus comes_A	81.897	278	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCA_000155875.1	s__Bariatricus comes	81.7795	283	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCF_003435815.1	s__CAG-317 sp000433215	81.6852	335	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.71	98.41	0.89	0.86	9	-
GCA_003480425.1	s__Schaedlerella sp900066545	81.2906	213	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.16	96.52	0.81	0.77	11	-
GCF_000169235.1	s__Dorea formicigenerans	81.1919	303	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea	95.0	97.68	96.97	0.80	0.73	43	-
GCF_003477705.1	s__Lachnoclostridium_B sp900066555	80.8293	247	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	97.98	96.92	0.87	0.81	6	-
GCF_000155205.1	s__Mediterraneibacter lactaris	79.97	181	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCA_000433535.1	s__CAG-317 sp000433535	79.0577	198	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.49	98.19	0.84	0.83	3	-
GCA_016295505.1	s__Dorea_A sp016295505	78.804	229	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543415.1	s__CAG-317 sp900543415	78.7787	195	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	97.35	95.87	0.87	0.78	4	-
GCF_000403455.2	s__Sporofaciens sp000403455	78.041	177	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.91	98.91	0.91	0.91	2	-
GCA_910579925.1	s__Sporofaciens sp910579925	76.8698	121	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:48,287] [INFO] GTDB search result was written to GCF_025567265.1_ASM2556726v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:48,288] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:48,291] [INFO] DFAST_QC result json was written to GCF_025567265.1_ASM2556726v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:48,292] [INFO] DFAST_QC completed!
[2024-01-25 17:41:48,292] [INFO] Total running time: 0h0m57s