[2023-06-13 03:03:15,667] [INFO] DFAST_QC pipeline started.
[2023-06-13 03:03:15,669] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 03:03:15,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fd1e068-f8c9-4c22-81d5-f8fac844766b/dqc_reference
[2023-06-13 03:03:16,872] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 03:03:16,873] [INFO] Task started: Prodigal
[2023-06-13 03:03:16,873] [INFO] Running command: gunzip -c /var/lib/cwl/stg69e17dde-7f83-42c2-9866-6be413e9afb8/GCA_022792105.1_ASM2279210v1_genomic.fna.gz | prodigal -d GCA_022792105.1_ASM2279210v1_genomic.fna/cds.fna -a GCA_022792105.1_ASM2279210v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 03:03:20,673] [INFO] Task succeeded: Prodigal
[2023-06-13 03:03:20,674] [INFO] Task started: HMMsearch
[2023-06-13 03:03:20,674] [INFO] Running command: hmmsearch --tblout GCA_022792105.1_ASM2279210v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fd1e068-f8c9-4c22-81d5-f8fac844766b/dqc_reference/reference_markers.hmm GCA_022792105.1_ASM2279210v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 03:03:20,821] [INFO] Task succeeded: HMMsearch
[2023-06-13 03:03:20,822] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg69e17dde-7f83-42c2-9866-6be413e9afb8/GCA_022792105.1_ASM2279210v1_genomic.fna.gz]
[2023-06-13 03:03:20,840] [INFO] Query marker FASTA was written to GCA_022792105.1_ASM2279210v1_genomic.fna/markers.fasta
[2023-06-13 03:03:20,840] [INFO] Task started: Blastn
[2023-06-13 03:03:20,840] [INFO] Running command: blastn -query GCA_022792105.1_ASM2279210v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fd1e068-f8c9-4c22-81d5-f8fac844766b/dqc_reference/reference_markers.fasta -out GCA_022792105.1_ASM2279210v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:03:21,427] [INFO] Task succeeded: Blastn
[2023-06-13 03:03:21,431] [INFO] Selected 15 target genomes.
[2023-06-13 03:03:21,431] [INFO] Target genome list was writen to GCA_022792105.1_ASM2279210v1_genomic.fna/target_genomes.txt
[2023-06-13 03:03:21,434] [INFO] Task started: fastANI
[2023-06-13 03:03:21,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg69e17dde-7f83-42c2-9866-6be413e9afb8/GCA_022792105.1_ASM2279210v1_genomic.fna.gz --refList GCA_022792105.1_ASM2279210v1_genomic.fna/target_genomes.txt --output GCA_022792105.1_ASM2279210v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 03:03:29,293] [INFO] Task succeeded: fastANI
[2023-06-13 03:03:29,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fd1e068-f8c9-4c22-81d5-f8fac844766b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 03:03:29,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fd1e068-f8c9-4c22-81d5-f8fac844766b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 03:03:29,304] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 03:03:29,304] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 03:03:29,304] [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
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	79.6402	214	441	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.3833	156	441	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.3403	153	441	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.0289	135	441	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.2229	97	441	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.0534	90	441	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	76.8086	74	441	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.6727	55	441	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.6159	75	441	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	76.4403	52	441	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	76.1783	51	441	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 03:03:29,306] [INFO] DFAST Taxonomy check result was written to GCA_022792105.1_ASM2279210v1_genomic.fna/tc_result.tsv
[2023-06-13 03:03:29,307] [INFO] ===== Taxonomy check completed =====
[2023-06-13 03:03:29,307] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 03:03:29,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fd1e068-f8c9-4c22-81d5-f8fac844766b/dqc_reference/checkm_data
[2023-06-13 03:03:29,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 03:03:29,328] [INFO] Task started: CheckM
[2023-06-13 03:03:29,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022792105.1_ASM2279210v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022792105.1_ASM2279210v1_genomic.fna/checkm_input GCA_022792105.1_ASM2279210v1_genomic.fna/checkm_result
[2023-06-13 03:03:46,567] [INFO] Task succeeded: CheckM
[2023-06-13 03:03:46,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 27.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 03:03:46,582] [INFO] ===== Completeness check finished =====
[2023-06-13 03:03:46,583] [INFO] ===== Start GTDB Search =====
[2023-06-13 03:03:46,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022792105.1_ASM2279210v1_genomic.fna/markers.fasta)
[2023-06-13 03:03:46,583] [INFO] Task started: Blastn
[2023-06-13 03:03:46,583] [INFO] Running command: blastn -query GCA_022792105.1_ASM2279210v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fd1e068-f8c9-4c22-81d5-f8fac844766b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022792105.1_ASM2279210v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:03:47,560] [INFO] Task succeeded: Blastn
[2023-06-13 03:03:47,564] [INFO] Selected 11 target genomes.
[2023-06-13 03:03:47,564] [INFO] Target genome list was writen to GCA_022792105.1_ASM2279210v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 03:03:47,568] [INFO] Task started: fastANI
[2023-06-13 03:03:47,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg69e17dde-7f83-42c2-9866-6be413e9afb8/GCA_022792105.1_ASM2279210v1_genomic.fna.gz --refList GCA_022792105.1_ASM2279210v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022792105.1_ASM2279210v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 03:03:53,488] [INFO] Task succeeded: fastANI
[2023-06-13 03:03:53,501] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 03:03:53,502] [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_910584605.1	s__Lawsonibacter sp910584605	98.7799	390	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910585815.1	s__Lawsonibacter sp910585815	85.3841	348	441	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_910578735.1	s__Lawsonibacter sp910578735	84.6682	315	441	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_910575265.1	s__Lawsonibacter sp910575265	84.1197	345	441	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_910588635.1	s__Lawsonibacter sp910588635	84.0852	331	441	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_910589085.1	s__Lawsonibacter sp910589085	84.007	304	441	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_009911645.1	s__Lawsonibacter sp009911645	83.4321	342	441	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_009917615.1	s__Lawsonibacter sp009917615	82.9485	337	441	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_900549405.1	s__Lawsonibacter sp900549405	80.4908	204	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.96	97.96	0.89	0.89	2	-
GCF_014287875.1	s__Lawsonibacter sp014287875	80.4335	221	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.47	96.91	0.89	0.83	4	-
GCF_003478995.1	s__Lawsonibacter sp003478995	80.3479	222	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-13 03:03:53,504] [INFO] GTDB search result was written to GCA_022792105.1_ASM2279210v1_genomic.fna/result_gtdb.tsv
[2023-06-13 03:03:53,504] [INFO] ===== GTDB Search completed =====
[2023-06-13 03:03:53,507] [INFO] DFAST_QC result json was written to GCA_022792105.1_ASM2279210v1_genomic.fna/dqc_result.json
[2023-06-13 03:03:53,508] [INFO] DFAST_QC completed!
[2023-06-13 03:03:53,508] [INFO] Total running time: 0h0m38s