[2023-06-28 06:39:41,396] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:39:41,402] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:39:41,403] [INFO] DQC Reference Directory: /var/lib/cwl/stgd769bc32-4e45-416e-b0db-5542987fb3b6/dqc_reference
[2023-06-28 06:39:42,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:39:42,965] [INFO] Task started: Prodigal
[2023-06-28 06:39:42,965] [INFO] Running command: gunzip -c /var/lib/cwl/stg88295059-2343-4b84-8987-bef1b8df3c96/GCA_944385565.1_BRZ_EB_bin11_genomic.fna.gz | prodigal -d GCA_944385565.1_BRZ_EB_bin11_genomic.fna/cds.fna -a GCA_944385565.1_BRZ_EB_bin11_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:39:49,124] [INFO] Task succeeded: Prodigal
[2023-06-28 06:39:49,125] [INFO] Task started: HMMsearch
[2023-06-28 06:39:49,125] [INFO] Running command: hmmsearch --tblout GCA_944385565.1_BRZ_EB_bin11_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd769bc32-4e45-416e-b0db-5542987fb3b6/dqc_reference/reference_markers.hmm GCA_944385565.1_BRZ_EB_bin11_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:39:49,364] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:39:49,365] [INFO] Found 6/6 markers.
[2023-06-28 06:39:49,399] [INFO] Query marker FASTA was written to GCA_944385565.1_BRZ_EB_bin11_genomic.fna/markers.fasta
[2023-06-28 06:39:49,400] [INFO] Task started: Blastn
[2023-06-28 06:39:49,400] [INFO] Running command: blastn -query GCA_944385565.1_BRZ_EB_bin11_genomic.fna/markers.fasta -db /var/lib/cwl/stgd769bc32-4e45-416e-b0db-5542987fb3b6/dqc_reference/reference_markers.fasta -out GCA_944385565.1_BRZ_EB_bin11_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:39:50,131] [INFO] Task succeeded: Blastn
[2023-06-28 06:39:50,135] [INFO] Selected 25 target genomes.
[2023-06-28 06:39:50,135] [INFO] Target genome list was writen to GCA_944385565.1_BRZ_EB_bin11_genomic.fna/target_genomes.txt
[2023-06-28 06:39:50,137] [INFO] Task started: fastANI
[2023-06-28 06:39:50,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg88295059-2343-4b84-8987-bef1b8df3c96/GCA_944385565.1_BRZ_EB_bin11_genomic.fna.gz --refList GCA_944385565.1_BRZ_EB_bin11_genomic.fna/target_genomes.txt --output GCA_944385565.1_BRZ_EB_bin11_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:40:03,893] [INFO] Task succeeded: fastANI
[2023-06-28 06:40:03,894] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd769bc32-4e45-416e-b0db-5542987fb3b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:40:03,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd769bc32-4e45-416e-b0db-5542987fb3b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:40:03,904] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:40:03,904] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 06:40:03,904] [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
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.0946	56	641	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	76.972	57	641	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.8667	66	641	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.8275	69	641	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.7922	69	641	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.7873	59	641	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.4118	71	641	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	76.1783	52	641	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 06:40:03,906] [INFO] DFAST Taxonomy check result was written to GCA_944385565.1_BRZ_EB_bin11_genomic.fna/tc_result.tsv
[2023-06-28 06:40:03,909] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:40:03,909] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:40:03,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd769bc32-4e45-416e-b0db-5542987fb3b6/dqc_reference/checkm_data
[2023-06-28 06:40:03,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:40:03,942] [INFO] Task started: CheckM
[2023-06-28 06:40:03,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944385565.1_BRZ_EB_bin11_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944385565.1_BRZ_EB_bin11_genomic.fna/checkm_input GCA_944385565.1_BRZ_EB_bin11_genomic.fna/checkm_result
[2023-06-28 06:40:27,980] [INFO] Task succeeded: CheckM
[2023-06-28 06:40:27,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:40:28,006] [INFO] ===== Completeness check finished =====
[2023-06-28 06:40:28,007] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:40:28,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944385565.1_BRZ_EB_bin11_genomic.fna/markers.fasta)
[2023-06-28 06:40:28,007] [INFO] Task started: Blastn
[2023-06-28 06:40:28,008] [INFO] Running command: blastn -query GCA_944385565.1_BRZ_EB_bin11_genomic.fna/markers.fasta -db /var/lib/cwl/stgd769bc32-4e45-416e-b0db-5542987fb3b6/dqc_reference/reference_markers_gtdb.fasta -out GCA_944385565.1_BRZ_EB_bin11_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:40:29,167] [INFO] Task succeeded: Blastn
[2023-06-28 06:40:29,173] [INFO] Selected 16 target genomes.
[2023-06-28 06:40:29,173] [INFO] Target genome list was writen to GCA_944385565.1_BRZ_EB_bin11_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:40:29,179] [INFO] Task started: fastANI
[2023-06-28 06:40:29,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg88295059-2343-4b84-8987-bef1b8df3c96/GCA_944385565.1_BRZ_EB_bin11_genomic.fna.gz --refList GCA_944385565.1_BRZ_EB_bin11_genomic.fna/target_genomes_gtdb.txt --output GCA_944385565.1_BRZ_EB_bin11_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:40:36,172] [INFO] Task succeeded: fastANI
[2023-06-28 06:40:36,192] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 06:40:36,192] [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_018712145.1	s__Faecousia faecigallinarum	98.792	529	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900545515.1	s__Faecousia sp000435995	78.7779	246	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.49	98.99	0.94	0.88	3	-
GCA_900544975.1	s__Faecousia sp900544975	78.7396	235	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.46	99.22	0.93	0.93	4	-
GCA_900546915.1	s__Faecousia gallistercoris	78.6968	180	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.45	99.22	0.91	0.80	6	-
GCA_018713285.1	s__Faecousia excrementigallinarum	77.8494	106	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712825.1	s__Faecousia excrementipullorum	77.7302	116	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.33	97.33	0.89	0.89	2	-
GCA_016302405.1	s__Faecousia sp016302405	77.5964	99	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713205.1	s__Avoscillospira stercorigallinarum	77.4538	111	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067725.1	s__Faecousia sp015067725	77.4505	124	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068455.1	s__Faecousia sp015068455	77.4461	86	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002437585.1	s__Faecousia sp002437585	77.3914	118	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.35	99.16	0.96	0.95	3	-
GCA_017622995.1	s__Faecousia sp017622995	77.3023	114	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589155.1	s__Faecousia sp910589155	77.2352	109	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904395865.1	s__Avoscillospira_A sp904395865	76.7984	80	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017473225.1	s__Faecousia sp017473225	76.798	81	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067845.1	s__Faecousia sp015067845	76.688	82	641	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 06:40:36,194] [INFO] GTDB search result was written to GCA_944385565.1_BRZ_EB_bin11_genomic.fna/result_gtdb.tsv
[2023-06-28 06:40:36,195] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:40:36,199] [INFO] DFAST_QC result json was written to GCA_944385565.1_BRZ_EB_bin11_genomic.fna/dqc_result.json
[2023-06-28 06:40:36,199] [INFO] DFAST_QC completed!
[2023-06-28 06:40:36,199] [INFO] Total running time: 0h0m55s