[2023-06-13 14:59:18,103] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:59:18,105] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:59:18,105] [INFO] DQC Reference Directory: /var/lib/cwl/stg316c4d30-df53-4f3c-9708-ee755e88869c/dqc_reference
[2023-06-13 14:59:19,408] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:59:19,410] [INFO] Task started: Prodigal
[2023-06-13 14:59:19,410] [INFO] Running command: gunzip -c /var/lib/cwl/stga6a93f8a-bd5f-4875-ac25-872996a9a28e/GCA_022774325.1_ASM2277432v1_genomic.fna.gz | prodigal -d GCA_022774325.1_ASM2277432v1_genomic.fna/cds.fna -a GCA_022774325.1_ASM2277432v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:59:25,881] [INFO] Task succeeded: Prodigal
[2023-06-13 14:59:25,881] [INFO] Task started: HMMsearch
[2023-06-13 14:59:25,881] [INFO] Running command: hmmsearch --tblout GCA_022774325.1_ASM2277432v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg316c4d30-df53-4f3c-9708-ee755e88869c/dqc_reference/reference_markers.hmm GCA_022774325.1_ASM2277432v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:59:26,148] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:59:26,150] [INFO] Found 6/6 markers.
[2023-06-13 14:59:26,180] [INFO] Query marker FASTA was written to GCA_022774325.1_ASM2277432v1_genomic.fna/markers.fasta
[2023-06-13 14:59:26,181] [INFO] Task started: Blastn
[2023-06-13 14:59:26,181] [INFO] Running command: blastn -query GCA_022774325.1_ASM2277432v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg316c4d30-df53-4f3c-9708-ee755e88869c/dqc_reference/reference_markers.fasta -out GCA_022774325.1_ASM2277432v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:59:26,872] [INFO] Task succeeded: Blastn
[2023-06-13 14:59:26,876] [INFO] Selected 26 target genomes.
[2023-06-13 14:59:26,877] [INFO] Target genome list was writen to GCA_022774325.1_ASM2277432v1_genomic.fna/target_genomes.txt
[2023-06-13 14:59:26,879] [INFO] Task started: fastANI
[2023-06-13 14:59:26,879] [INFO] Running command: fastANI --query /var/lib/cwl/stga6a93f8a-bd5f-4875-ac25-872996a9a28e/GCA_022774325.1_ASM2277432v1_genomic.fna.gz --refList GCA_022774325.1_ASM2277432v1_genomic.fna/target_genomes.txt --output GCA_022774325.1_ASM2277432v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:59:40,017] [INFO] Task succeeded: fastANI
[2023-06-13 14:59:40,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg316c4d30-df53-4f3c-9708-ee755e88869c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:59:40,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg316c4d30-df53-4f3c-9708-ee755e88869c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:59:40,041] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:59:40,041] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:59:40,041] [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
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	78.6537	255	855	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.9775	125	855	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.9398	124	855	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.8559	124	855	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	77.7718	115	855	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	77.6086	149	855	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	77.5664	151	855	95	below_threshold
Sellimonas caecigallum	strain=SW451	GCA_019754295.1	2592333	2592333	type	True	77.5554	120	855	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.4281	124	855	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	77.3598	89	855	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	77.2835	60	855	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	77.2806	79	855	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	77.2171	89	855	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	77.2049	78	855	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	77.124	62	855	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	77.1013	130	855	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	77.094	60	855	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	77.0894	127	855	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	76.9617	76	855	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	76.9575	84	855	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.8616	90	855	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	76.8218	92	855	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	76.5426	64	855	95	below_threshold
Coprococcus catus	strain=ATCC 27761	GCA_025289135.1	116085	116085	suspected-type	True	76.3067	72	855	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:59:40,044] [INFO] DFAST Taxonomy check result was written to GCA_022774325.1_ASM2277432v1_genomic.fna/tc_result.tsv
[2023-06-13 14:59:40,044] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:59:40,044] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:59:40,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg316c4d30-df53-4f3c-9708-ee755e88869c/dqc_reference/checkm_data
[2023-06-13 14:59:40,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:59:40,077] [INFO] Task started: CheckM
[2023-06-13 14:59:40,077] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022774325.1_ASM2277432v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022774325.1_ASM2277432v1_genomic.fna/checkm_input GCA_022774325.1_ASM2277432v1_genomic.fna/checkm_result
[2023-06-13 15:00:06,606] [INFO] Task succeeded: CheckM
[2023-06-13 15:00:06,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:00:06,636] [INFO] ===== Completeness check finished =====
[2023-06-13 15:00:06,636] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:00:06,636] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022774325.1_ASM2277432v1_genomic.fna/markers.fasta)
[2023-06-13 15:00:06,637] [INFO] Task started: Blastn
[2023-06-13 15:00:06,637] [INFO] Running command: blastn -query GCA_022774325.1_ASM2277432v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg316c4d30-df53-4f3c-9708-ee755e88869c/dqc_reference/reference_markers_gtdb.fasta -out GCA_022774325.1_ASM2277432v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:00:07,711] [INFO] Task succeeded: Blastn
[2023-06-13 15:00:07,759] [INFO] Selected 19 target genomes.
[2023-06-13 15:00:07,759] [INFO] Target genome list was writen to GCA_022774325.1_ASM2277432v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:00:07,768] [INFO] Task started: fastANI
[2023-06-13 15:00:07,769] [INFO] Running command: fastANI --query /var/lib/cwl/stga6a93f8a-bd5f-4875-ac25-872996a9a28e/GCA_022774325.1_ASM2277432v1_genomic.fna.gz --refList GCA_022774325.1_ASM2277432v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022774325.1_ASM2277432v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:00:16,460] [INFO] Task succeeded: fastANI
[2023-06-13 15:00:16,482] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:00:16,482] [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_004560705.1	s__Bariatricus sp004560705	99.2777	624	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.19	99.19	0.81	0.81	2	conclusive
GCA_004562915.1	s__Oliverpabstia sp004562915	84.9557	136	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013300725.1	s__Bariatricus comes_A	78.9489	249	855	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	78.6447	245	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCA_905216215.1	s__Bariatricus sp905216215	78.1148	115	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554415.1	s__Bariatricus sp900554415	78.0912	114	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.94	99.94	0.94	0.94	2	-
GCF_002159995.1	s__Sellimonas sp002159995	77.5219	125	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sellimonas	95.0	99.10	98.94	0.88	0.83	3	-
GCA_003489085.1	s__UBA9414 sp003489085	77.4782	87	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016295505.1	s__Dorea_A sp016295505	77.3531	137	855	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_905203555.1	s__Schaedlerella sp905203555	77.3406	92	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900312975.1	s__Massilistercora timonensis	77.2405	77	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Massilistercora	95.0	95.86	95.52	0.90	0.88	4	-
GCA_001312505.1	s__Mediterraneibacter faecis	77.1147	127	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.72	95.03	0.76	0.67	61	-
GCF_000169235.1	s__Dorea formicigenerans	77.1025	126	855	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_002159505.1	s__Mediterraneibacter ornithocaccae	77.0474	92	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.93	97.52	0.83	0.82	3	-
GCA_900765975.1	s__Schaedlerella sp900765975	76.8223	84	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.94	99.94	0.80	0.80	2	-
GCA_019118885.1	s__Mediterraneibacter surreyensis	76.7189	82	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.86	98.12	0.80	0.76	3	-
GCA_900553355.1	s__Merdimonas sp900553355	76.6848	105	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 15:00:16,484] [INFO] GTDB search result was written to GCA_022774325.1_ASM2277432v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:00:16,485] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:00:16,491] [INFO] DFAST_QC result json was written to GCA_022774325.1_ASM2277432v1_genomic.fna/dqc_result.json
[2023-06-13 15:00:16,491] [INFO] DFAST_QC completed!
[2023-06-13 15:00:16,491] [INFO] Total running time: 0h0m58s