[2023-06-28 17:35:33,513] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:35:33,516] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:35:33,517] [INFO] DQC Reference Directory: /var/lib/cwl/stg4db7b098-8666-4514-929c-efdf84e7ddec/dqc_reference
[2023-06-28 17:35:35,926] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:35:35,927] [INFO] Task started: Prodigal
[2023-06-28 17:35:35,927] [INFO] Running command: gunzip -c /var/lib/cwl/stgca1b5c3e-61b1-4cb9-aba1-5ab62cd883b3/GCA_944385125.1_BRZ_DM_bin54_genomic.fna.gz | prodigal -d GCA_944385125.1_BRZ_DM_bin54_genomic.fna/cds.fna -a GCA_944385125.1_BRZ_DM_bin54_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:35:41,252] [INFO] Task succeeded: Prodigal
[2023-06-28 17:35:41,253] [INFO] Task started: HMMsearch
[2023-06-28 17:35:41,253] [INFO] Running command: hmmsearch --tblout GCA_944385125.1_BRZ_DM_bin54_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4db7b098-8666-4514-929c-efdf84e7ddec/dqc_reference/reference_markers.hmm GCA_944385125.1_BRZ_DM_bin54_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:35:41,477] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:35:41,479] [INFO] Found 6/6 markers.
[2023-06-28 17:35:41,503] [INFO] Query marker FASTA was written to GCA_944385125.1_BRZ_DM_bin54_genomic.fna/markers.fasta
[2023-06-28 17:35:41,504] [INFO] Task started: Blastn
[2023-06-28 17:35:41,504] [INFO] Running command: blastn -query GCA_944385125.1_BRZ_DM_bin54_genomic.fna/markers.fasta -db /var/lib/cwl/stg4db7b098-8666-4514-929c-efdf84e7ddec/dqc_reference/reference_markers.fasta -out GCA_944385125.1_BRZ_DM_bin54_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:35:42,117] [INFO] Task succeeded: Blastn
[2023-06-28 17:35:42,122] [INFO] Selected 13 target genomes.
[2023-06-28 17:35:42,122] [INFO] Target genome list was writen to GCA_944385125.1_BRZ_DM_bin54_genomic.fna/target_genomes.txt
[2023-06-28 17:35:42,124] [INFO] Task started: fastANI
[2023-06-28 17:35:42,124] [INFO] Running command: fastANI --query /var/lib/cwl/stgca1b5c3e-61b1-4cb9-aba1-5ab62cd883b3/GCA_944385125.1_BRZ_DM_bin54_genomic.fna.gz --refList GCA_944385125.1_BRZ_DM_bin54_genomic.fna/target_genomes.txt --output GCA_944385125.1_BRZ_DM_bin54_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:35:48,516] [INFO] Task succeeded: fastANI
[2023-06-28 17:35:48,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4db7b098-8666-4514-929c-efdf84e7ddec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:35:48,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4db7b098-8666-4514-929c-efdf84e7ddec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:35:48,531] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:35:48,531] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:35:48,531] [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
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.3126	111	631	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.2709	104	631	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.268	99	631	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.2523	103	631	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.2287	81	631	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.1988	64	631	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.0707	86	631	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	76.8503	71	631	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	76.8099	70	631	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	76.7979	55	631	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:35:48,533] [INFO] DFAST Taxonomy check result was written to GCA_944385125.1_BRZ_DM_bin54_genomic.fna/tc_result.tsv
[2023-06-28 17:35:48,534] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:35:48,534] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:35:48,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4db7b098-8666-4514-929c-efdf84e7ddec/dqc_reference/checkm_data
[2023-06-28 17:35:48,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:35:48,557] [INFO] Task started: CheckM
[2023-06-28 17:35:48,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944385125.1_BRZ_DM_bin54_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944385125.1_BRZ_DM_bin54_genomic.fna/checkm_input GCA_944385125.1_BRZ_DM_bin54_genomic.fna/checkm_result
[2023-06-28 17:36:10,058] [INFO] Task succeeded: CheckM
[2023-06-28 17:36:10,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:36:10,084] [INFO] ===== Completeness check finished =====
[2023-06-28 17:36:10,084] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:36:10,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944385125.1_BRZ_DM_bin54_genomic.fna/markers.fasta)
[2023-06-28 17:36:10,085] [INFO] Task started: Blastn
[2023-06-28 17:36:10,085] [INFO] Running command: blastn -query GCA_944385125.1_BRZ_DM_bin54_genomic.fna/markers.fasta -db /var/lib/cwl/stg4db7b098-8666-4514-929c-efdf84e7ddec/dqc_reference/reference_markers_gtdb.fasta -out GCA_944385125.1_BRZ_DM_bin54_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:36:11,036] [INFO] Task succeeded: Blastn
[2023-06-28 17:36:11,041] [INFO] Selected 16 target genomes.
[2023-06-28 17:36:11,042] [INFO] Target genome list was writen to GCA_944385125.1_BRZ_DM_bin54_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:36:11,074] [INFO] Task started: fastANI
[2023-06-28 17:36:11,075] [INFO] Running command: fastANI --query /var/lib/cwl/stgca1b5c3e-61b1-4cb9-aba1-5ab62cd883b3/GCA_944385125.1_BRZ_DM_bin54_genomic.fna.gz --refList GCA_944385125.1_BRZ_DM_bin54_genomic.fna/target_genomes_gtdb.txt --output GCA_944385125.1_BRZ_DM_bin54_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:36:18,240] [INFO] Task succeeded: fastANI
[2023-06-28 17:36:18,256] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:36:18,257] [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_018711755.1	s__Limivicinus faecipullorum	90.1521	428	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754515.1	s__Limivicinus sp900754515	84.0624	423	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.83	97.83	0.85	0.85	2	-
GCA_004560305.1	s__Limivicinus sp004560305	81.9275	283	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	96.68	96.68	0.69	0.69	2	-
GCA_900316255.1	s__Limivicinus sp900316255	79.463	191	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.92	95.41	0.88	0.79	4	-
GCA_017428565.1	s__Limivicinus sp017428565	79.3822	193	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775355.1	s__Limivicinus sp902775355	79.1655	216	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902787755.1	s__Limivicinus sp902787755	79.0744	186	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316205.1	s__Limivicinus sp900316205	79.0555	196	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.11	98.31	0.88	0.81	3	-
GCA_017545165.1	s__Limivicinus sp017545165	78.7756	179	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458085.1	s__Limivicinus sp017458085	78.7569	184	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320035.1	s__Limivicinus sp002320035	78.5173	170	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.95	98.71	0.80	0.75	5	-
GCA_902793285.1	s__Limivicinus sp902793285	78.4738	152	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.34	97.34	0.78	0.78	2	-
GCA_902779945.1	s__Limivicinus sp902779945	78.4462	163	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319695.1	s__Limivicinus sp900319695	78.1815	169	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.29	96.47	0.86	0.81	8	-
GCA_902789745.1	s__Limivicinus sp902789745	77.713	150	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546515.1	s__Limivicinus sp900546515	77.4568	118	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.98	99.98	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-28 17:36:18,260] [INFO] GTDB search result was written to GCA_944385125.1_BRZ_DM_bin54_genomic.fna/result_gtdb.tsv
[2023-06-28 17:36:18,261] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:36:18,264] [INFO] DFAST_QC result json was written to GCA_944385125.1_BRZ_DM_bin54_genomic.fna/dqc_result.json
[2023-06-28 17:36:18,265] [INFO] DFAST_QC completed!
[2023-06-28 17:36:18,265] [INFO] Total running time: 0h0m45s