[2024-01-24 15:02:33,490] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:33,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:33,492] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb0d2f2a-9ff3-485f-8623-4918bd513c60/dqc_reference
[2024-01-24 15:02:34,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:34,754] [INFO] Task started: Prodigal
[2024-01-24 15:02:34,754] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c03127e-52c1-430d-8a11-c8cc4f0185dc/GCF_003425665.1_ASM342566v1_genomic.fna.gz | prodigal -d GCF_003425665.1_ASM342566v1_genomic.fna/cds.fna -a GCF_003425665.1_ASM342566v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:42,060] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:42,060] [INFO] Task started: HMMsearch
[2024-01-24 15:02:42,060] [INFO] Running command: hmmsearch --tblout GCF_003425665.1_ASM342566v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb0d2f2a-9ff3-485f-8623-4918bd513c60/dqc_reference/reference_markers.hmm GCF_003425665.1_ASM342566v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:42,357] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:42,359] [INFO] Found 6/6 markers.
[2024-01-24 15:02:42,386] [INFO] Query marker FASTA was written to GCF_003425665.1_ASM342566v1_genomic.fna/markers.fasta
[2024-01-24 15:02:42,387] [INFO] Task started: Blastn
[2024-01-24 15:02:42,387] [INFO] Running command: blastn -query GCF_003425665.1_ASM342566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb0d2f2a-9ff3-485f-8623-4918bd513c60/dqc_reference/reference_markers.fasta -out GCF_003425665.1_ASM342566v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:43,053] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:43,055] [INFO] Selected 13 target genomes.
[2024-01-24 15:02:43,056] [INFO] Target genome list was writen to GCF_003425665.1_ASM342566v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:43,062] [INFO] Task started: fastANI
[2024-01-24 15:02:43,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c03127e-52c1-430d-8a11-c8cc4f0185dc/GCF_003425665.1_ASM342566v1_genomic.fna.gz --refList GCF_003425665.1_ASM342566v1_genomic.fna/target_genomes.txt --output GCF_003425665.1_ASM342566v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:50,461] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:50,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb0d2f2a-9ff3-485f-8623-4918bd513c60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:50,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb0d2f2a-9ff3-485f-8623-4918bd513c60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:50,472] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:02:50,472] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:50,472] [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
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	100.0	799	803	95	conclusive
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	100.0	799	803	95	conclusive
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	82.5411	54	803	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	82.4286	54	803	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.8408	170	803	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.7683	89	803	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.5014	161	803	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.4334	153	803	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.2242	134	803	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.8842	158	803	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.8346	98	803	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:50,476] [INFO] DFAST Taxonomy check result was written to GCF_003425665.1_ASM342566v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:50,476] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:50,476] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:50,477] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb0d2f2a-9ff3-485f-8623-4918bd513c60/dqc_reference/checkm_data
[2024-01-24 15:02:50,478] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:50,509] [INFO] Task started: CheckM
[2024-01-24 15:02:50,510] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003425665.1_ASM342566v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003425665.1_ASM342566v1_genomic.fna/checkm_input GCF_003425665.1_ASM342566v1_genomic.fna/checkm_result
[2024-01-24 15:03:18,929] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:18,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:18,950] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:18,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:18,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003425665.1_ASM342566v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:18,951] [INFO] Task started: Blastn
[2024-01-24 15:03:18,951] [INFO] Running command: blastn -query GCF_003425665.1_ASM342566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb0d2f2a-9ff3-485f-8623-4918bd513c60/dqc_reference/reference_markers_gtdb.fasta -out GCF_003425665.1_ASM342566v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:20,121] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:20,124] [INFO] Selected 11 target genomes.
[2024-01-24 15:03:20,125] [INFO] Target genome list was writen to GCF_003425665.1_ASM342566v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:20,148] [INFO] Task started: fastANI
[2024-01-24 15:03:20,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c03127e-52c1-430d-8a11-c8cc4f0185dc/GCF_003425665.1_ASM342566v1_genomic.fna.gz --refList GCF_003425665.1_ASM342566v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003425665.1_ASM342566v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:26,149] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:26,165] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:26,165] [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_003425665.1	s__Evtepia gabavorous	100.0	799	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	99.51	98.88	0.95	0.87	8	conclusive
GCA_004554585.1	s__Evtepia sp004554585	82.7349	460	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.56	98.47	0.94	0.93	3	-
GCA_019115545.1	s__Evtepia faecavium	82.6451	403	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546255.1	s__Evtepia excrementipullorum	82.4298	419	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.07	97.85	0.89	0.87	5	-
GCA_019115225.1	s__Evtepia faecigallinarum	82.4241	421	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004551945.1	s__Evtepia sp004551945	81.5108	407	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.68	98.58	0.91	0.88	5	-
GCA_004556345.1	s__Evtepia sp004556345	81.33	329	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.03	97.32	0.86	0.79	7	-
GCA_016296565.1	s__Evtepia sp016296565	81.3164	340	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781745.1	s__Evtepia sp902781745	80.8968	295	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.13	97.74	0.85	0.79	11	-
GCA_016295225.1	s__Evtepia sp016295225	80.5124	291	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435425.1	s__Evtepia sp017435425	79.9962	312	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.49	98.49	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:26,168] [INFO] GTDB search result was written to GCF_003425665.1_ASM342566v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:26,174] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:26,180] [INFO] DFAST_QC result json was written to GCF_003425665.1_ASM342566v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:26,181] [INFO] DFAST_QC completed!
[2024-01-24 15:03:26,181] [INFO] Total running time: 0h0m53s