[2023-06-28 22:25:01,857] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:25:01,861] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:25:01,861] [INFO] DQC Reference Directory: /var/lib/cwl/stgee59f86b-da92-4edc-94fa-ae1dc6b088c9/dqc_reference
[2023-06-28 22:25:03,145] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:25:03,145] [INFO] Task started: Prodigal
[2023-06-28 22:25:03,146] [INFO] Running command: gunzip -c /var/lib/cwl/stg071600ec-f10a-44b5-9337-a53caaf078a4/GCA_020025455.1_ASM2002545v1_genomic.fna.gz | prodigal -d GCA_020025455.1_ASM2002545v1_genomic.fna/cds.fna -a GCA_020025455.1_ASM2002545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:25:06,735] [INFO] Task succeeded: Prodigal
[2023-06-28 22:25:06,736] [INFO] Task started: HMMsearch
[2023-06-28 22:25:06,736] [INFO] Running command: hmmsearch --tblout GCA_020025455.1_ASM2002545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee59f86b-da92-4edc-94fa-ae1dc6b088c9/dqc_reference/reference_markers.hmm GCA_020025455.1_ASM2002545v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:25:06,952] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:25:06,953] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg071600ec-f10a-44b5-9337-a53caaf078a4/GCA_020025455.1_ASM2002545v1_genomic.fna.gz]
[2023-06-28 22:25:06,975] [INFO] Query marker FASTA was written to GCA_020025455.1_ASM2002545v1_genomic.fna/markers.fasta
[2023-06-28 22:25:06,975] [INFO] Task started: Blastn
[2023-06-28 22:25:06,975] [INFO] Running command: blastn -query GCA_020025455.1_ASM2002545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee59f86b-da92-4edc-94fa-ae1dc6b088c9/dqc_reference/reference_markers.fasta -out GCA_020025455.1_ASM2002545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:25:07,627] [INFO] Task succeeded: Blastn
[2023-06-28 22:25:07,632] [INFO] Selected 17 target genomes.
[2023-06-28 22:25:07,632] [INFO] Target genome list was writen to GCA_020025455.1_ASM2002545v1_genomic.fna/target_genomes.txt
[2023-06-28 22:25:07,634] [INFO] Task started: fastANI
[2023-06-28 22:25:07,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg071600ec-f10a-44b5-9337-a53caaf078a4/GCA_020025455.1_ASM2002545v1_genomic.fna.gz --refList GCA_020025455.1_ASM2002545v1_genomic.fna/target_genomes.txt --output GCA_020025455.1_ASM2002545v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:25:14,606] [INFO] Task succeeded: fastANI
[2023-06-28 22:25:14,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee59f86b-da92-4edc-94fa-ae1dc6b088c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:25:14,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee59f86b-da92-4edc-94fa-ae1dc6b088c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:25:14,618] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:25:14,618] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:25:14,618] [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	79.7056	182	388	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.919	138	388	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.9093	134	388	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.8502	137	388	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	78.6269	62	388	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	78.0724	77	388	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.9819	97	388	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.8106	80	388	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.8	103	388	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	77.7935	103	388	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.7682	100	388	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.5033	59	388	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	77.1361	65	388	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	77.0984	66	388	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:25:14,621] [INFO] DFAST Taxonomy check result was written to GCA_020025455.1_ASM2002545v1_genomic.fna/tc_result.tsv
[2023-06-28 22:25:14,622] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:25:14,622] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:25:14,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee59f86b-da92-4edc-94fa-ae1dc6b088c9/dqc_reference/checkm_data
[2023-06-28 22:25:14,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:25:14,645] [INFO] Task started: CheckM
[2023-06-28 22:25:14,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020025455.1_ASM2002545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020025455.1_ASM2002545v1_genomic.fna/checkm_input GCA_020025455.1_ASM2002545v1_genomic.fna/checkm_result
[2023-06-28 22:25:33,027] [INFO] Task succeeded: CheckM
[2023-06-28 22:25:33,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 3.03%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:25:33,054] [INFO] ===== Completeness check finished =====
[2023-06-28 22:25:33,054] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:25:33,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020025455.1_ASM2002545v1_genomic.fna/markers.fasta)
[2023-06-28 22:25:33,055] [INFO] Task started: Blastn
[2023-06-28 22:25:33,055] [INFO] Running command: blastn -query GCA_020025455.1_ASM2002545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee59f86b-da92-4edc-94fa-ae1dc6b088c9/dqc_reference/reference_markers_gtdb.fasta -out GCA_020025455.1_ASM2002545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:25:34,161] [INFO] Task succeeded: Blastn
[2023-06-28 22:25:34,166] [INFO] Selected 23 target genomes.
[2023-06-28 22:25:34,167] [INFO] Target genome list was writen to GCA_020025455.1_ASM2002545v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:25:34,198] [INFO] Task started: fastANI
[2023-06-28 22:25:34,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg071600ec-f10a-44b5-9337-a53caaf078a4/GCA_020025455.1_ASM2002545v1_genomic.fna.gz --refList GCA_020025455.1_ASM2002545v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020025455.1_ASM2002545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:25:44,360] [INFO] Task succeeded: fastANI
[2023-06-28 22:25:44,381] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 22:25:44,381] [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_014287875.1	s__Lawsonibacter sp014287875	80.9486	211	388	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	80.8766	224	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900550705.1	s__Lawsonibacter sp900550705	80.8758	178	388	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_016899775.1	s__Lawsonibacter sp900545895	80.4541	196	388	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_900553135.1	s__Lawsonibacter sp900553135	80.4284	173	388	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_002160305.1	s__Lawsonibacter pullicola	80.2538	204	388	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_002161175.1	s__Lawsonibacter sp002161175	80.2164	195	388	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_008727735.1	s__Lawsonibacter sp000177015	80.0682	212	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	96.97	96.84	0.88	0.83	6	-
GCA_900549405.1	s__Lawsonibacter sp900549405	80.0559	190	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.96	97.96	0.89	0.89	2	-
GCA_017624915.1	s__Lawsonibacter sp017624915	79.9756	141	388	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_003612335.1	s__Lawsonibacter sp003612335	79.622	177	388	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	79.5936	190	388	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_900626285.1	s__Flavonifractor massiliensis_A	79.4857	146	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009911645.1	s__Lawsonibacter sp009911645	79.3962	183	388	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_017811815.1	s__Flavonifractor sp017811815	79.356	153	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589085.1	s__Lawsonibacter sp910589085	79.3321	176	388	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_015068065.1	s__Lawsonibacter sp015068065	79.1488	106	388	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_016901735.1	s__An92 sp016901735	79.0344	127	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.81	98.81	0.85	0.85	2	-
GCF_900199495.1	s__An92 sp900199495	78.8828	139	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.28	97.84	0.85	0.79	7	-
GCA_014799505.1	s__Enterenecus sp014799505	78.2637	75	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118935.1	s__Dysosmobacter pullicola	78.1317	101	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.04	97.82	0.81	0.80	3	-
GCA_905215425.1	s__Lawsonibacter sp905215425	78.0185	79	388	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_019115225.1	s__Evtepia faecigallinarum	77.9667	86	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:25:44,383] [INFO] GTDB search result was written to GCA_020025455.1_ASM2002545v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:25:44,384] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:25:44,388] [INFO] DFAST_QC result json was written to GCA_020025455.1_ASM2002545v1_genomic.fna/dqc_result.json
[2023-06-28 22:25:44,388] [INFO] DFAST_QC completed!
[2023-06-28 22:25:44,388] [INFO] Total running time: 0h0m43s