[2023-06-16 22:13:19,529] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:13:19,537] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:13:19,538] [INFO] DQC Reference Directory: /var/lib/cwl/stgad76ee53-1867-48ce-bbfb-b0c18098c844/dqc_reference
[2023-06-16 22:13:20,767] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:13:20,768] [INFO] Task started: Prodigal
[2023-06-16 22:13:20,768] [INFO] Running command: gunzip -c /var/lib/cwl/stg10f847d2-be16-4af4-ad25-d68ee10f7e53/GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna.gz | prodigal -d GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/cds.fna -a GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:13:26,257] [INFO] Task succeeded: Prodigal
[2023-06-16 22:13:26,257] [INFO] Task started: HMMsearch
[2023-06-16 22:13:26,257] [INFO] Running command: hmmsearch --tblout GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad76ee53-1867-48ce-bbfb-b0c18098c844/dqc_reference/reference_markers.hmm GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:13:26,481] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:13:26,482] [INFO] Found 6/6 markers.
[2023-06-16 22:13:26,501] [INFO] Query marker FASTA was written to GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/markers.fasta
[2023-06-16 22:13:26,502] [INFO] Task started: Blastn
[2023-06-16 22:13:26,502] [INFO] Running command: blastn -query GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/markers.fasta -db /var/lib/cwl/stgad76ee53-1867-48ce-bbfb-b0c18098c844/dqc_reference/reference_markers.fasta -out GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:13:27,211] [INFO] Task succeeded: Blastn
[2023-06-16 22:13:27,215] [INFO] Selected 15 target genomes.
[2023-06-16 22:13:27,215] [INFO] Target genome list was writen to GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/target_genomes.txt
[2023-06-16 22:13:27,232] [INFO] Task started: fastANI
[2023-06-16 22:13:27,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg10f847d2-be16-4af4-ad25-d68ee10f7e53/GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna.gz --refList GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/target_genomes.txt --output GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:13:34,992] [INFO] Task succeeded: fastANI
[2023-06-16 22:13:34,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad76ee53-1867-48ce-bbfb-b0c18098c844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:13:34,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad76ee53-1867-48ce-bbfb-b0c18098c844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:13:35,008] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 22:13:35,009] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 22:13:35,009] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	82.5773	345	608	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	80.984	277	608	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	79.2183	220	608	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.8206	182	608	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.4232	146	608	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.3172	153	608	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.1144	122	608	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.7217	102	608	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.5829	104	608	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	77.2677	63	608	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	77.0966	80	608	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 22:13:35,011] [INFO] DFAST Taxonomy check result was written to GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/tc_result.tsv
[2023-06-16 22:13:35,012] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:13:35,012] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:13:35,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad76ee53-1867-48ce-bbfb-b0c18098c844/dqc_reference/checkm_data
[2023-06-16 22:13:35,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:13:35,040] [INFO] Task started: CheckM
[2023-06-16 22:13:35,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/checkm_input GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/checkm_result
[2023-06-16 22:13:57,264] [INFO] Task succeeded: CheckM
[2023-06-16 22:13:57,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 22:13:57,293] [INFO] ===== Completeness check finished =====
[2023-06-16 22:13:57,294] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:13:57,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/markers.fasta)
[2023-06-16 22:13:57,295] [INFO] Task started: Blastn
[2023-06-16 22:13:57,295] [INFO] Running command: blastn -query GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/markers.fasta -db /var/lib/cwl/stgad76ee53-1867-48ce-bbfb-b0c18098c844/dqc_reference/reference_markers_gtdb.fasta -out GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:13:58,623] [INFO] Task succeeded: Blastn
[2023-06-16 22:13:58,628] [INFO] Selected 16 target genomes.
[2023-06-16 22:13:58,628] [INFO] Target genome list was writen to GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:13:58,650] [INFO] Task started: fastANI
[2023-06-16 22:13:58,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg10f847d2-be16-4af4-ad25-d68ee10f7e53/GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna.gz --refList GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/target_genomes_gtdb.txt --output GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:14:05,511] [INFO] Task succeeded: fastANI
[2023-06-16 22:14:05,531] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 22:14:05,531] [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_000435975.1	s__CAG-83 sp000435975	97.8041	490	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.04	97.67	0.83	0.76	8	conclusive
GCA_018228685.1	s__CAG-83 sp001916855	91.9519	492	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	96.79	95.43	0.86	0.74	11	-
GCF_018408575.1	s__CAG-83 sp000431575	82.6184	347	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.84	97.37	0.92	0.86	9	-
GCA_900551355.1	s__CAG-83 sp900551355	82.4165	241	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.94	98.90	0.93	0.92	3	-
GCA_900545495.1	s__CAG-83 sp900545495	81.6769	320	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.95	95.34	0.89	0.84	5	-
GCA_902388735.1	s__CAG-83 sp902388735	81.5021	269	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.86	98.86	0.87	0.87	2	-
GCA_900552725.1	s__CAG-83 sp900552725	81.454	263	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.50	98.05	0.78	0.74	4	-
GCA_900317425.1	s__CAG-83 sp900317425	81.4521	266	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.98	99.98	0.95	0.95	2	-
GCA_900547745.1	s__CAG-83 sp900547745	81.4366	282	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.22	99.21	0.93	0.91	3	-
GCA_900545585.1	s__CAG-83 sp900545585	81.4249	308	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.41	98.11	0.88	0.81	5	-
GCA_017427645.1	s__CAG-83 sp017427645	81.1377	249	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018326305.1	s__CAG-83 sp900549395	81.015	274	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.26	97.06	0.85	0.74	6	-
GCA_900554275.1	s__CAG-83 sp900554275	81.0091	255	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.46	96.91	0.80	0.75	4	-
GCA_015068325.1	s__CAG-83 sp015068325	80.4553	245	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017415775.1	s__CAG-83 sp017415775	79.3505	194	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905210385.1	s__Enterenecus sp905210385	79.0022	63	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 22:14:05,534] [INFO] GTDB search result was written to GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/result_gtdb.tsv
[2023-06-16 22:14:05,534] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:14:05,539] [INFO] DFAST_QC result json was written to GCA_905199845.1_SRR5558303-mag-bin.53_genomic.fna/dqc_result.json
[2023-06-16 22:14:05,539] [INFO] DFAST_QC completed!
[2023-06-16 22:14:05,539] [INFO] Total running time: 0h0m46s