[2024-01-24 13:17:34,417] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,421] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,421] [INFO] DQC Reference Directory: /var/lib/cwl/stgc290460f-01e9-4d98-97e2-858a00822b98/dqc_reference
[2024-01-24 13:17:35,801] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:35,802] [INFO] Task started: Prodigal
[2024-01-24 13:17:35,802] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b5b0f17-230b-4169-b4db-e4e4081b2d6c/GCF_002201515.1_ASM220151v1_genomic.fna.gz | prodigal -d GCF_002201515.1_ASM220151v1_genomic.fna/cds.fna -a GCF_002201515.1_ASM220151v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:55,810] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:55,810] [INFO] Task started: HMMsearch
[2024-01-24 13:17:55,810] [INFO] Running command: hmmsearch --tblout GCF_002201515.1_ASM220151v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc290460f-01e9-4d98-97e2-858a00822b98/dqc_reference/reference_markers.hmm GCF_002201515.1_ASM220151v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:56,091] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:56,092] [INFO] Found 6/6 markers.
[2024-01-24 13:17:56,122] [INFO] Query marker FASTA was written to GCF_002201515.1_ASM220151v1_genomic.fna/markers.fasta
[2024-01-24 13:17:56,122] [INFO] Task started: Blastn
[2024-01-24 13:17:56,122] [INFO] Running command: blastn -query GCF_002201515.1_ASM220151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc290460f-01e9-4d98-97e2-858a00822b98/dqc_reference/reference_markers.fasta -out GCF_002201515.1_ASM220151v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:56,733] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:56,736] [INFO] Selected 9 target genomes.
[2024-01-24 13:17:56,737] [INFO] Target genome list was writen to GCF_002201515.1_ASM220151v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:56,741] [INFO] Task started: fastANI
[2024-01-24 13:17:56,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b5b0f17-230b-4169-b4db-e4e4081b2d6c/GCF_002201515.1_ASM220151v1_genomic.fna.gz --refList GCF_002201515.1_ASM220151v1_genomic.fna/target_genomes.txt --output GCF_002201515.1_ASM220151v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:05,526] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:05,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc290460f-01e9-4d98-97e2-858a00822b98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:05,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc290460f-01e9-4d98-97e2-858a00822b98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:05,535] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:18:05,535] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:05,535] [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
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	100.0	1099	1102	95	conclusive
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	99.9993	1099	1102	95	conclusive
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	99.9962	1097	1102	95	conclusive
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	82.8409	140	1102	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	82.3068	140	1102	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	80.5308	213	1102	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	79.1965	133	1102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:05,537] [INFO] DFAST Taxonomy check result was written to GCF_002201515.1_ASM220151v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:05,537] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:05,538] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:05,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc290460f-01e9-4d98-97e2-858a00822b98/dqc_reference/checkm_data
[2024-01-24 13:18:05,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:05,574] [INFO] Task started: CheckM
[2024-01-24 13:18:05,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002201515.1_ASM220151v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002201515.1_ASM220151v1_genomic.fna/checkm_input GCF_002201515.1_ASM220151v1_genomic.fna/checkm_result
[2024-01-24 13:19:03,708] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:03,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:03,731] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:03,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:03,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002201515.1_ASM220151v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:03,733] [INFO] Task started: Blastn
[2024-01-24 13:19:03,733] [INFO] Running command: blastn -query GCF_002201515.1_ASM220151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc290460f-01e9-4d98-97e2-858a00822b98/dqc_reference/reference_markers_gtdb.fasta -out GCF_002201515.1_ASM220151v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:04,687] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:04,692] [INFO] Selected 23 target genomes.
[2024-01-24 13:19:04,692] [INFO] Target genome list was writen to GCF_002201515.1_ASM220151v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:04,757] [INFO] Task started: fastANI
[2024-01-24 13:19:04,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b5b0f17-230b-4169-b4db-e4e4081b2d6c/GCF_002201515.1_ASM220151v1_genomic.fna.gz --refList GCF_002201515.1_ASM220151v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002201515.1_ASM220151v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:16,919] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:16,940] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:16,941] [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_002201515.1	s__Muribaculum intestinale	100.0	1101	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.09	97.90	0.92	0.80	20	conclusive
GCF_004803915.1	s__Duncaniella dubosii	82.3162	140	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.46	96.11	0.91	0.80	8	-
GCF_004803695.1	s__Muribaculum gordoncarteri	80.3802	206	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	96.82	95.63	0.92	0.83	15	-
GCA_004102785.1	s__UBA7173 sp002491305	80.1207	158	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.18	98.68	0.94	0.92	6	-
GCA_910583865.1	s__Muribaculum sp910583865	79.6911	425	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004102805.1	s__UBA7173 sp004102805	79.5668	145	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	98.86	98.86	0.92	0.89	3	-
GCA_910578835.1	s__Muribaculum sp910578835	78.0107	172	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584825.1	s__Duncaniella sp910584825	77.9783	131	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905193485.1	s__Paramuribaculum sp905193485	77.8711	73	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009775605.1	s__Paramuribaculum sp009775605	77.7891	108	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	99.73	99.73	0.91	0.91	2	-
GCA_003150235.1	s__Muribaculum sp003150235	77.6983	154	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	97.90	96.97	0.85	0.80	6	-
GCA_001689405.1	s__Muribaculum arabinoxylanisolvens	77.6819	150	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.46	99.01	0.94	0.92	3	-
GCA_910587665.1	s__Muribaculum sp910587665	77.6201	139	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009775095.1	s__Muribaculum sp009775095	77.6067	152	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.95	99.95	0.97	0.97	2	-
GCA_014801485.1	s__CAG-873 sp014801485	77.5547	77	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689445.1	s__M3 sp001689445	77.552	131	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__M3	95.0	99.97	99.97	0.98	0.98	2	-
GCA_905210435.1	s__UBA7173 sp905210435	77.4826	127	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001915385.1	s__UBA7173 sp001915385	77.4821	127	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	96.67	96.43	0.78	0.73	4	-
GCA_910578785.1	s__Muribaculum sp910578785	77.3899	159	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586995.1	s__CAG-873 sp910586995	77.3096	80	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541865.1	s__CAG-873 sp900541865	77.2748	80	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009177195.1	s__Muribaculum sp009177195	77.0161	91	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587075.1	s__UBA7173 sp910587075	76.9261	105	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:16,944] [INFO] GTDB search result was written to GCF_002201515.1_ASM220151v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:16,944] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:16,948] [INFO] DFAST_QC result json was written to GCF_002201515.1_ASM220151v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:16,948] [INFO] DFAST_QC completed!
[2024-01-24 13:19:16,948] [INFO] Total running time: 0h1m43s