[2023-06-19 04:44:12,328] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:44:12,345] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:44:12,346] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe6ab87c-6db2-49fd-9bb3-7df26bf6a1ee/dqc_reference
[2023-06-19 04:44:13,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:44:13,681] [INFO] Task started: Prodigal
[2023-06-19 04:44:13,682] [INFO] Running command: gunzip -c /var/lib/cwl/stge86633c3-65b0-465c-972a-c1d3ce5ed19b/GCA_018366795.1_ASM1836679v1_genomic.fna.gz | prodigal -d GCA_018366795.1_ASM1836679v1_genomic.fna/cds.fna -a GCA_018366795.1_ASM1836679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:44:20,871] [INFO] Task succeeded: Prodigal
[2023-06-19 04:44:20,871] [INFO] Task started: HMMsearch
[2023-06-19 04:44:20,872] [INFO] Running command: hmmsearch --tblout GCA_018366795.1_ASM1836679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe6ab87c-6db2-49fd-9bb3-7df26bf6a1ee/dqc_reference/reference_markers.hmm GCA_018366795.1_ASM1836679v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:44:21,116] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:44:21,117] [INFO] Found 6/6 markers.
[2023-06-19 04:44:21,141] [INFO] Query marker FASTA was written to GCA_018366795.1_ASM1836679v1_genomic.fna/markers.fasta
[2023-06-19 04:44:21,142] [INFO] Task started: Blastn
[2023-06-19 04:44:21,142] [INFO] Running command: blastn -query GCA_018366795.1_ASM1836679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe6ab87c-6db2-49fd-9bb3-7df26bf6a1ee/dqc_reference/reference_markers.fasta -out GCA_018366795.1_ASM1836679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:44:21,861] [INFO] Task succeeded: Blastn
[2023-06-19 04:44:21,865] [INFO] Selected 16 target genomes.
[2023-06-19 04:44:21,865] [INFO] Target genome list was writen to GCA_018366795.1_ASM1836679v1_genomic.fna/target_genomes.txt
[2023-06-19 04:44:21,868] [INFO] Task started: fastANI
[2023-06-19 04:44:21,868] [INFO] Running command: fastANI --query /var/lib/cwl/stge86633c3-65b0-465c-972a-c1d3ce5ed19b/GCA_018366795.1_ASM1836679v1_genomic.fna.gz --refList GCA_018366795.1_ASM1836679v1_genomic.fna/target_genomes.txt --output GCA_018366795.1_ASM1836679v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:44:31,399] [INFO] Task succeeded: fastANI
[2023-06-19 04:44:31,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe6ab87c-6db2-49fd-9bb3-7df26bf6a1ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:44:31,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe6ab87c-6db2-49fd-9bb3-7df26bf6a1ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:44:31,413] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:44:31,413] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 04:44:31,414] [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	81.611	410	803	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	79.9762	289	803	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	79.8716	289	803	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	79.5726	277	803	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.5537	204	803	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	78.4288	184	803	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	78.4043	187	803	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	78.0873	150	803	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.892	154	803	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.668	120	803	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.5879	146	803	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	77.029	92	803	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	77.0028	93	803	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 04:44:31,416] [INFO] DFAST Taxonomy check result was written to GCA_018366795.1_ASM1836679v1_genomic.fna/tc_result.tsv
[2023-06-19 04:44:31,417] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:44:31,417] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:44:31,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe6ab87c-6db2-49fd-9bb3-7df26bf6a1ee/dqc_reference/checkm_data
[2023-06-19 04:44:31,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:44:31,456] [INFO] Task started: CheckM
[2023-06-19 04:44:31,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018366795.1_ASM1836679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018366795.1_ASM1836679v1_genomic.fna/checkm_input GCA_018366795.1_ASM1836679v1_genomic.fna/checkm_result
[2023-06-19 04:44:58,112] [INFO] Task succeeded: CheckM
[2023-06-19 04:44:58,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:44:58,133] [INFO] ===== Completeness check finished =====
[2023-06-19 04:44:58,134] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:44:58,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018366795.1_ASM1836679v1_genomic.fna/markers.fasta)
[2023-06-19 04:44:58,134] [INFO] Task started: Blastn
[2023-06-19 04:44:58,135] [INFO] Running command: blastn -query GCA_018366795.1_ASM1836679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe6ab87c-6db2-49fd-9bb3-7df26bf6a1ee/dqc_reference/reference_markers_gtdb.fasta -out GCA_018366795.1_ASM1836679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:44:59,387] [INFO] Task succeeded: Blastn
[2023-06-19 04:44:59,390] [INFO] Selected 10 target genomes.
[2023-06-19 04:44:59,391] [INFO] Target genome list was writen to GCA_018366795.1_ASM1836679v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:44:59,394] [INFO] Task started: fastANI
[2023-06-19 04:44:59,394] [INFO] Running command: fastANI --query /var/lib/cwl/stge86633c3-65b0-465c-972a-c1d3ce5ed19b/GCA_018366795.1_ASM1836679v1_genomic.fna.gz --refList GCA_018366795.1_ASM1836679v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018366795.1_ASM1836679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:45:06,017] [INFO] Task succeeded: fastANI
[2023-06-19 04:45:06,026] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:45:06,026] [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_003573975.1	s__Lawsonibacter sp900066825	99.2172	720	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.28	97.95	0.82	0.77	5	conclusive
GCA_902363045.1	s__Lawsonibacter sp902363045	92.8666	671	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.07	97.96	0.86	0.80	4	-
GCA_900764755.1	s__Lawsonibacter sp900764755	91.8496	596	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	99.46	99.46	0.86	0.86	2	-
GCA_900754605.1	s__Lawsonibacter sp900754605	87.4473	481	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.97	98.72	0.79	0.78	3	-
GCF_002160305.1	s__Lawsonibacter pullicola	83.5477	504	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.22	97.83	0.90	0.75	8	-
GCF_016899775.1	s__Lawsonibacter sp900545895	83.4332	496	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	96.62	96.12	0.85	0.79	4	-
GCA_905205085.1	s__Lawsonibacter sp900766145	81.7066	376	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	99.79	99.79	0.87	0.87	2	-
GCA_003112755.1	s__Lawsonibacter asaccharolyticus	81.4395	407	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.88	98.69	0.87	0.78	6	-
GCA_904420465.1	s__Lawsonibacter sp904420465	81.2674	337	803	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	80.5698	312	803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:45:06,028] [INFO] GTDB search result was written to GCA_018366795.1_ASM1836679v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:45:06,029] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:45:06,032] [INFO] DFAST_QC result json was written to GCA_018366795.1_ASM1836679v1_genomic.fna/dqc_result.json
[2023-06-19 04:45:06,033] [INFO] DFAST_QC completed!
[2023-06-19 04:45:06,033] [INFO] Total running time: 0h0m54s