[2023-06-28 08:04:23,492] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:04:23,495] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:04:23,496] [INFO] DQC Reference Directory: /var/lib/cwl/stge36ae456-853c-490f-b527-2dab536b3d14/dqc_reference
[2023-06-28 08:04:25,815] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:04:25,816] [INFO] Task started: Prodigal
[2023-06-28 08:04:25,816] [INFO] Running command: gunzip -c /var/lib/cwl/stg95b57809-19b4-4c2f-af58-86d5d66a40df/GCA_944385175.1_BRZ_NA_bin27_genomic.fna.gz | prodigal -d GCA_944385175.1_BRZ_NA_bin27_genomic.fna/cds.fna -a GCA_944385175.1_BRZ_NA_bin27_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:04:31,408] [INFO] Task succeeded: Prodigal
[2023-06-28 08:04:31,409] [INFO] Task started: HMMsearch
[2023-06-28 08:04:31,409] [INFO] Running command: hmmsearch --tblout GCA_944385175.1_BRZ_NA_bin27_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge36ae456-853c-490f-b527-2dab536b3d14/dqc_reference/reference_markers.hmm GCA_944385175.1_BRZ_NA_bin27_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:04:31,638] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:04:31,640] [INFO] Found 6/6 markers.
[2023-06-28 08:04:31,665] [INFO] Query marker FASTA was written to GCA_944385175.1_BRZ_NA_bin27_genomic.fna/markers.fasta
[2023-06-28 08:04:31,665] [INFO] Task started: Blastn
[2023-06-28 08:04:31,665] [INFO] Running command: blastn -query GCA_944385175.1_BRZ_NA_bin27_genomic.fna/markers.fasta -db /var/lib/cwl/stge36ae456-853c-490f-b527-2dab536b3d14/dqc_reference/reference_markers.fasta -out GCA_944385175.1_BRZ_NA_bin27_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:04:32,242] [INFO] Task succeeded: Blastn
[2023-06-28 08:04:32,247] [INFO] Selected 16 target genomes.
[2023-06-28 08:04:32,247] [INFO] Target genome list was writen to GCA_944385175.1_BRZ_NA_bin27_genomic.fna/target_genomes.txt
[2023-06-28 08:04:32,251] [INFO] Task started: fastANI
[2023-06-28 08:04:32,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg95b57809-19b4-4c2f-af58-86d5d66a40df/GCA_944385175.1_BRZ_NA_bin27_genomic.fna.gz --refList GCA_944385175.1_BRZ_NA_bin27_genomic.fna/target_genomes.txt --output GCA_944385175.1_BRZ_NA_bin27_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:04:39,564] [INFO] Task succeeded: fastANI
[2023-06-28 08:04:39,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge36ae456-853c-490f-b527-2dab536b3d14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:04:39,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge36ae456-853c-490f-b527-2dab536b3d14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:04:39,579] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:04:39,579] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 08:04:39,580] [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	77.5138	75	669	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.3905	74	669	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.3122	60	669	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.2099	69	669	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.0981	59	669	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.8535	73	669	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.8502	56	669	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	76.5297	58	669	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 08:04:39,581] [INFO] DFAST Taxonomy check result was written to GCA_944385175.1_BRZ_NA_bin27_genomic.fna/tc_result.tsv
[2023-06-28 08:04:39,582] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:04:39,582] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:04:39,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge36ae456-853c-490f-b527-2dab536b3d14/dqc_reference/checkm_data
[2023-06-28 08:04:39,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:04:39,609] [INFO] Task started: CheckM
[2023-06-28 08:04:39,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944385175.1_BRZ_NA_bin27_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944385175.1_BRZ_NA_bin27_genomic.fna/checkm_input GCA_944385175.1_BRZ_NA_bin27_genomic.fna/checkm_result
[2023-06-28 08:05:02,220] [INFO] Task succeeded: CheckM
[2023-06-28 08:05:02,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:05:02,243] [INFO] ===== Completeness check finished =====
[2023-06-28 08:05:02,243] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:05:02,244] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944385175.1_BRZ_NA_bin27_genomic.fna/markers.fasta)
[2023-06-28 08:05:02,244] [INFO] Task started: Blastn
[2023-06-28 08:05:02,244] [INFO] Running command: blastn -query GCA_944385175.1_BRZ_NA_bin27_genomic.fna/markers.fasta -db /var/lib/cwl/stge36ae456-853c-490f-b527-2dab536b3d14/dqc_reference/reference_markers_gtdb.fasta -out GCA_944385175.1_BRZ_NA_bin27_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:05:03,045] [INFO] Task succeeded: Blastn
[2023-06-28 08:05:03,049] [INFO] Selected 21 target genomes.
[2023-06-28 08:05:03,049] [INFO] Target genome list was writen to GCA_944385175.1_BRZ_NA_bin27_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:05:03,169] [INFO] Task started: fastANI
[2023-06-28 08:05:03,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg95b57809-19b4-4c2f-af58-86d5d66a40df/GCA_944385175.1_BRZ_NA_bin27_genomic.fna.gz --refList GCA_944385175.1_BRZ_NA_bin27_genomic.fna/target_genomes_gtdb.txt --output GCA_944385175.1_BRZ_NA_bin27_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:05:12,572] [INFO] Task succeeded: fastANI
[2023-06-28 08:05:12,600] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 08:05:12,601] [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	86.6652	400	669	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	85.1118	466	669	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	81.0203	286	669	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_017458085.1	s__Limivicinus sp017458085	79.2519	150	669	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_902778275.1	s__Limivicinus sp902778275	78.9309	174	669	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_017470325.1	s__Limivicinus sp017470325	78.8692	165	669	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_900319635.1	s__Limivicinus sp900319635	78.8084	156	669	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.84	96.83	0.85	0.76	6	-
GCA_900316255.1	s__Limivicinus sp900316255	78.7317	155	669	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_017545165.1	s__Limivicinus sp017545165	78.5984	122	669	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_900549545.1	s__Limivicinus sp900549545	78.5232	155	669	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.92	99.84	0.93	0.88	3	-
GCA_902775355.1	s__Limivicinus sp902775355	78.5227	170	669	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_900547315.1	s__Limivicinus sp900547315	78.4036	113	669	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.47	98.42	0.88	0.83	3	-
GCA_902765595.1	s__Limivicinus sp002350825	78.3621	144	669	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.80	99.80	0.90	0.90	2	-
GCA_900549865.1	s__Limivicinus sp900549865	78.3364	116	669	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.13	98.09	0.79	0.79	3	-
GCA_902785905.1	s__Limivicinus sp902785905	78.2904	123	669	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_900321275.1	s__Limivicinus sp900321275	78.1588	123	669	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.70	95.66	0.85	0.80	7	-
GCA_900319695.1	s__Limivicinus sp900319695	78.1366	133	669	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_902802215.1	s__Limivicinus sp902802215	78.0603	117	669	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.44	98.44	0.76	0.76	2	-
GCA_002320035.1	s__Limivicinus sp002320035	78.0482	155	669	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_902766405.1	s__Limivicinus sp902766405	76.5745	59	669	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_905234425.1	s__HGM13006 sp905234425	76.0992	53	669	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__HGM13006	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 08:05:12,603] [INFO] GTDB search result was written to GCA_944385175.1_BRZ_NA_bin27_genomic.fna/result_gtdb.tsv
[2023-06-28 08:05:12,604] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:05:12,608] [INFO] DFAST_QC result json was written to GCA_944385175.1_BRZ_NA_bin27_genomic.fna/dqc_result.json
[2023-06-28 08:05:12,608] [INFO] DFAST_QC completed!
[2023-06-28 08:05:12,608] [INFO] Total running time: 0h0m49s