[2023-06-17 05:04:40,908] [INFO] DFAST_QC pipeline started.
[2023-06-17 05:04:40,919] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 05:04:40,919] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f3c14eb-6cfc-4e8a-8936-587e675c0a11/dqc_reference
[2023-06-17 05:04:42,353] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 05:04:42,354] [INFO] Task started: Prodigal
[2023-06-17 05:04:42,354] [INFO] Running command: gunzip -c /var/lib/cwl/stg0210e825-2359-469f-a709-9715b0fda493/GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna.gz | prodigal -d GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/cds.fna -a GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 05:04:48,285] [INFO] Task succeeded: Prodigal
[2023-06-17 05:04:48,286] [INFO] Task started: HMMsearch
[2023-06-17 05:04:48,286] [INFO] Running command: hmmsearch --tblout GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f3c14eb-6cfc-4e8a-8936-587e675c0a11/dqc_reference/reference_markers.hmm GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/protein.faa > /dev/null
[2023-06-17 05:04:48,559] [INFO] Task succeeded: HMMsearch
[2023-06-17 05:04:48,560] [INFO] Found 6/6 markers.
[2023-06-17 05:04:48,591] [INFO] Query marker FASTA was written to GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/markers.fasta
[2023-06-17 05:04:48,594] [INFO] Task started: Blastn
[2023-06-17 05:04:48,594] [INFO] Running command: blastn -query GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f3c14eb-6cfc-4e8a-8936-587e675c0a11/dqc_reference/reference_markers.fasta -out GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:04:49,337] [INFO] Task succeeded: Blastn
[2023-06-17 05:04:49,341] [INFO] Selected 17 target genomes.
[2023-06-17 05:04:49,342] [INFO] Target genome list was writen to GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/target_genomes.txt
[2023-06-17 05:04:49,346] [INFO] Task started: fastANI
[2023-06-17 05:04:49,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg0210e825-2359-469f-a709-9715b0fda493/GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna.gz --refList GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/target_genomes.txt --output GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 05:05:00,767] [INFO] Task succeeded: fastANI
[2023-06-17 05:05:00,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f3c14eb-6cfc-4e8a-8936-587e675c0a11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 05:05:00,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f3c14eb-6cfc-4e8a-8936-587e675c0a11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 05:05:00,777] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 05:05:00,777] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 05:05:00,777] [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
Butyricicoccus faecihominis	strain=JCM 31056	GCA_016586375.1	1712515	1712515	type	True	83.4046	428	711	95	below_threshold
Butyricicoccus faecihominis	strain=JCM 31056	GCA_014648015.1	1712515	1712515	type	True	83.3244	432	711	95	below_threshold
Agathobaculum desmolans	strain=ATCC 43058	GCA_000701665.1	39484	39484	type	True	79.4883	258	711	95	below_threshold
Intestinibacillus massiliensis	strain=type strain: Marseille-P3216	GCA_900155735.1	1871029	1871029	type	True	78.9088	217	711	95	below_threshold
Butyricicoccus pullicaecorum	strain=DSM 23266	GCA_900167005.1	501571	501571	type	True	78.4169	197	711	95	below_threshold
Butyricicoccus porcorum	strain=BB10	GCA_002157465.1	1945634	1945634	type	True	77.8992	115	711	95	below_threshold
Butyricicoccus intestinisimiae	strain=MSJd-7	GCA_018918345.1	2841509	2841509	type	True	77.3432	108	711	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.8489	61	711	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 05:05:00,780] [INFO] DFAST Taxonomy check result was written to GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/tc_result.tsv
[2023-06-17 05:05:00,780] [INFO] ===== Taxonomy check completed =====
[2023-06-17 05:05:00,780] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 05:05:00,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f3c14eb-6cfc-4e8a-8936-587e675c0a11/dqc_reference/checkm_data
[2023-06-17 05:05:00,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 05:05:00,812] [INFO] Task started: CheckM
[2023-06-17 05:05:00,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/checkm_input GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/checkm_result
[2023-06-17 05:05:24,830] [INFO] Task succeeded: CheckM
[2023-06-17 05:05:24,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 05:05:24,856] [INFO] ===== Completeness check finished =====
[2023-06-17 05:05:24,856] [INFO] ===== Start GTDB Search =====
[2023-06-17 05:05:24,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/markers.fasta)
[2023-06-17 05:05:24,857] [INFO] Task started: Blastn
[2023-06-17 05:05:24,857] [INFO] Running command: blastn -query GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f3c14eb-6cfc-4e8a-8936-587e675c0a11/dqc_reference/reference_markers_gtdb.fasta -out GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:05:26,209] [INFO] Task succeeded: Blastn
[2023-06-17 05:05:26,214] [INFO] Selected 13 target genomes.
[2023-06-17 05:05:26,214] [INFO] Target genome list was writen to GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 05:05:26,226] [INFO] Task started: fastANI
[2023-06-17 05:05:26,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg0210e825-2359-469f-a709-9715b0fda493/GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna.gz --refList GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/target_genomes_gtdb.txt --output GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 05:05:32,071] [INFO] Task succeeded: fastANI
[2023-06-17 05:05:32,082] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 05:05:32,082] [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_900544475.1	s__Agathobaculum sp900544475	97.5747	492	711	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.90	97.82	0.89	0.86	3	conclusive
GCF_003481705.1	s__Agathobaculum sp003481705	89.2384	571	711	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.33	96.26	0.92	0.82	8	-
GCA_003096535.1	s__Agathobaculum butyriciproducens	83.2822	432	711	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	96.66	95.68	0.85	0.79	34	-
GCA_900555465.1	s__Agathobaculum intestinigallinarum	81.0544	238	711	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.06	97.06	0.83	0.83	2	-
GCF_900625105.1	s__Agathobaculum sp900625105	81.0526	367	711	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113065.1	s__Agathobaculum stercoravium	80.7483	317	711	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.25	98.25	0.89	0.89	2	-
GCA_019115615.1	s__Agathobaculum merdavium	80.381	293	711	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114345.1	s__Agathobaculum pullistercoris	80.1457	296	711	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.72	98.13	0.86	0.78	4	-
GCA_019115425.1	s__Agathobaculum merdigallinarum	80.0786	278	711	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557315.1	s__Agathobaculum sp900557315	80.0532	222	711	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	100.00	100.00	0.98	0.98	2	-
GCF_002161595.1	s__Fournierella sp002161595	76.1431	55	711	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	98.81	98.81	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-17 05:05:32,084] [INFO] GTDB search result was written to GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/result_gtdb.tsv
[2023-06-17 05:05:32,085] [INFO] ===== GTDB Search completed =====
[2023-06-17 05:05:32,089] [INFO] DFAST_QC result json was written to GCA_905208735.1_ERR1600596-mag-bin.7_genomic.fna/dqc_result.json
[2023-06-17 05:05:32,089] [INFO] DFAST_QC completed!
[2023-06-17 05:05:32,089] [INFO] Total running time: 0h0m51s