[2023-06-28 23:25:50,819] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:25:50,821] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:25:50,822] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaa3a2ee-e344-436e-a96a-391df081fb47/dqc_reference
[2023-06-28 23:25:52,050] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:25:52,051] [INFO] Task started: Prodigal
[2023-06-28 23:25:52,051] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f0b9673-2bb1-40ff-805a-d93535869286/GCA_944387795.1_BRZ_NS_bin63_genomic.fna.gz | prodigal -d GCA_944387795.1_BRZ_NS_bin63_genomic.fna/cds.fna -a GCA_944387795.1_BRZ_NS_bin63_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:25:58,459] [INFO] Task succeeded: Prodigal
[2023-06-28 23:25:58,459] [INFO] Task started: HMMsearch
[2023-06-28 23:25:58,459] [INFO] Running command: hmmsearch --tblout GCA_944387795.1_BRZ_NS_bin63_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaa3a2ee-e344-436e-a96a-391df081fb47/dqc_reference/reference_markers.hmm GCA_944387795.1_BRZ_NS_bin63_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:25:58,706] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:25:58,707] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2f0b9673-2bb1-40ff-805a-d93535869286/GCA_944387795.1_BRZ_NS_bin63_genomic.fna.gz]
[2023-06-28 23:25:58,731] [INFO] Query marker FASTA was written to GCA_944387795.1_BRZ_NS_bin63_genomic.fna/markers.fasta
[2023-06-28 23:25:58,732] [INFO] Task started: Blastn
[2023-06-28 23:25:58,732] [INFO] Running command: blastn -query GCA_944387795.1_BRZ_NS_bin63_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaa3a2ee-e344-436e-a96a-391df081fb47/dqc_reference/reference_markers.fasta -out GCA_944387795.1_BRZ_NS_bin63_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:25:59,401] [INFO] Task succeeded: Blastn
[2023-06-28 23:25:59,404] [INFO] Selected 17 target genomes.
[2023-06-28 23:25:59,405] [INFO] Target genome list was writen to GCA_944387795.1_BRZ_NS_bin63_genomic.fna/target_genomes.txt
[2023-06-28 23:25:59,414] [INFO] Task started: fastANI
[2023-06-28 23:25:59,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f0b9673-2bb1-40ff-805a-d93535869286/GCA_944387795.1_BRZ_NS_bin63_genomic.fna.gz --refList GCA_944387795.1_BRZ_NS_bin63_genomic.fna/target_genomes.txt --output GCA_944387795.1_BRZ_NS_bin63_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:26:08,756] [INFO] Task succeeded: fastANI
[2023-06-28 23:26:08,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaa3a2ee-e344-436e-a96a-391df081fb47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:26:08,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaa3a2ee-e344-436e-a96a-391df081fb47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:26:08,770] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:26:08,771] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:26:08,771] [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
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.6425	140	741	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.4238	145	741	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.4216	111	741	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.2949	122	741	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.8727	99	741	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.8468	133	741	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.7173	125	741	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.2984	93	741	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.2761	92	741	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	76.9303	104	741	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:26:08,773] [INFO] DFAST Taxonomy check result was written to GCA_944387795.1_BRZ_NS_bin63_genomic.fna/tc_result.tsv
[2023-06-28 23:26:08,774] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:26:08,774] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:26:08,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaa3a2ee-e344-436e-a96a-391df081fb47/dqc_reference/checkm_data
[2023-06-28 23:26:08,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:26:08,804] [INFO] Task started: CheckM
[2023-06-28 23:26:08,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944387795.1_BRZ_NS_bin63_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944387795.1_BRZ_NS_bin63_genomic.fna/checkm_input GCA_944387795.1_BRZ_NS_bin63_genomic.fna/checkm_result
[2023-06-28 23:26:34,071] [INFO] Task succeeded: CheckM
[2023-06-28 23:26:34,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.90%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 23:26:34,096] [INFO] ===== Completeness check finished =====
[2023-06-28 23:26:34,096] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:26:34,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944387795.1_BRZ_NS_bin63_genomic.fna/markers.fasta)
[2023-06-28 23:26:34,097] [INFO] Task started: Blastn
[2023-06-28 23:26:34,097] [INFO] Running command: blastn -query GCA_944387795.1_BRZ_NS_bin63_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaa3a2ee-e344-436e-a96a-391df081fb47/dqc_reference/reference_markers_gtdb.fasta -out GCA_944387795.1_BRZ_NS_bin63_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:26:35,261] [INFO] Task succeeded: Blastn
[2023-06-28 23:26:35,266] [INFO] Selected 18 target genomes.
[2023-06-28 23:26:35,266] [INFO] Target genome list was writen to GCA_944387795.1_BRZ_NS_bin63_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:26:35,356] [INFO] Task started: fastANI
[2023-06-28 23:26:35,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f0b9673-2bb1-40ff-805a-d93535869286/GCA_944387795.1_BRZ_NS_bin63_genomic.fna.gz --refList GCA_944387795.1_BRZ_NS_bin63_genomic.fna/target_genomes_gtdb.txt --output GCA_944387795.1_BRZ_NS_bin63_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:26:44,032] [INFO] Task succeeded: fastANI
[2023-06-28 23:26:44,045] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:26:44,046] [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_900549475.1	s__Pelethomonas sp900549475	98.4333	623	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	97.96	97.93	0.83	0.81	3	conclusive
GCA_017887695.1	s__Pelethomonas sp017887695	84.3178	449	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712665.1	s__Pelethomonas intestinigallinarum	80.8431	262	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	97.99	97.70	0.89	0.81	4	-
GCA_902373635.1	s__Pelethomonas sp902373635	80.6564	337	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579965.1	s__Pelethomonas sp910579965	79.9374	285	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588365.1	s__Pelethomonas sp910588365	79.6766	284	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555795.1	s__Pelethomonas sp900555795	79.4216	169	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774055.1	s__Pelethomonas sp009774055	79.0601	221	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	97.62	97.62	0.73	0.73	2	-
GCF_002159175.1	s__An92 sp002159175	78.905	160	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.91	98.91	0.91	0.91	2	-
GCA_910583885.1	s__Pelethomonas sp910583885	78.8114	263	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901955.1	s__Flavonifractor phocaeensis_A	78.8044	146	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905205085.1	s__Lawsonibacter sp900766145	78.5373	113	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	99.79	99.79	0.87	0.87	2	-
GCF_002161175.1	s__Lawsonibacter sp002161175	78.5144	115	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553135.1	s__Lawsonibacter sp900553135	78.4498	123	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727735.1	s__Lawsonibacter sp000177015	78.3632	152	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	96.97	96.84	0.88	0.83	6	-
GCA_900550685.1	s__Dysosmobacter sp900550685	77.7684	127	741	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.83	98.83	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-06-28 23:26:44,048] [INFO] GTDB search result was written to GCA_944387795.1_BRZ_NS_bin63_genomic.fna/result_gtdb.tsv
[2023-06-28 23:26:44,048] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:26:44,052] [INFO] DFAST_QC result json was written to GCA_944387795.1_BRZ_NS_bin63_genomic.fna/dqc_result.json
[2023-06-28 23:26:44,052] [INFO] DFAST_QC completed!
[2023-06-28 23:26:44,052] [INFO] Total running time: 0h0m53s