[2023-06-13 00:10:01,042] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:10:01,052] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:10:01,052] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e40087f-4bad-4577-b40b-6e7597f01ae6/dqc_reference
[2023-06-13 00:10:03,458] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:10:03,459] [INFO] Task started: Prodigal
[2023-06-13 00:10:03,459] [INFO] Running command: gunzip -c /var/lib/cwl/stg63b729ea-5469-4ba0-81b9-c331aeadc846/GCA_022720955.1_ASM2272095v1_genomic.fna.gz | prodigal -d GCA_022720955.1_ASM2272095v1_genomic.fna/cds.fna -a GCA_022720955.1_ASM2272095v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:10:09,870] [INFO] Task succeeded: Prodigal
[2023-06-13 00:10:09,870] [INFO] Task started: HMMsearch
[2023-06-13 00:10:09,870] [INFO] Running command: hmmsearch --tblout GCA_022720955.1_ASM2272095v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e40087f-4bad-4577-b40b-6e7597f01ae6/dqc_reference/reference_markers.hmm GCA_022720955.1_ASM2272095v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:10:10,070] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:10:10,072] [INFO] Found 6/6 markers.
[2023-06-13 00:10:10,095] [INFO] Query marker FASTA was written to GCA_022720955.1_ASM2272095v1_genomic.fna/markers.fasta
[2023-06-13 00:10:10,096] [INFO] Task started: Blastn
[2023-06-13 00:10:10,096] [INFO] Running command: blastn -query GCA_022720955.1_ASM2272095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e40087f-4bad-4577-b40b-6e7597f01ae6/dqc_reference/reference_markers.fasta -out GCA_022720955.1_ASM2272095v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:10:10,816] [INFO] Task succeeded: Blastn
[2023-06-13 00:10:10,821] [INFO] Selected 15 target genomes.
[2023-06-13 00:10:10,822] [INFO] Target genome list was writen to GCA_022720955.1_ASM2272095v1_genomic.fna/target_genomes.txt
[2023-06-13 00:10:10,826] [INFO] Task started: fastANI
[2023-06-13 00:10:10,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg63b729ea-5469-4ba0-81b9-c331aeadc846/GCA_022720955.1_ASM2272095v1_genomic.fna.gz --refList GCA_022720955.1_ASM2272095v1_genomic.fna/target_genomes.txt --output GCA_022720955.1_ASM2272095v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:10:17,694] [INFO] Task succeeded: fastANI
[2023-06-13 00:10:17,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e40087f-4bad-4577-b40b-6e7597f01ae6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:10:17,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e40087f-4bad-4577-b40b-6e7597f01ae6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:10:17,712] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:10:17,712] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 00:10:17,712] [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
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	94.5499	605	674	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	94.4984	605	674	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.4776	608	674	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.4287	230	674	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.8318	258	674	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.708	247	674	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.6365	261	674	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.5498	226	674	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.5452	241	674	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.4584	173	674	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.2268	205	674	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 00:10:17,714] [INFO] DFAST Taxonomy check result was written to GCA_022720955.1_ASM2272095v1_genomic.fna/tc_result.tsv
[2023-06-13 00:10:17,715] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:10:17,715] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:10:17,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e40087f-4bad-4577-b40b-6e7597f01ae6/dqc_reference/checkm_data
[2023-06-13 00:10:17,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:10:17,740] [INFO] Task started: CheckM
[2023-06-13 00:10:17,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022720955.1_ASM2272095v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022720955.1_ASM2272095v1_genomic.fna/checkm_input GCA_022720955.1_ASM2272095v1_genomic.fna/checkm_result
[2023-06-13 00:10:42,169] [INFO] Task succeeded: CheckM
[2023-06-13 00:10:42,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:10:42,198] [INFO] ===== Completeness check finished =====
[2023-06-13 00:10:42,199] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:10:42,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022720955.1_ASM2272095v1_genomic.fna/markers.fasta)
[2023-06-13 00:10:42,200] [INFO] Task started: Blastn
[2023-06-13 00:10:42,200] [INFO] Running command: blastn -query GCA_022720955.1_ASM2272095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e40087f-4bad-4577-b40b-6e7597f01ae6/dqc_reference/reference_markers_gtdb.fasta -out GCA_022720955.1_ASM2272095v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:10:43,542] [INFO] Task succeeded: Blastn
[2023-06-13 00:10:43,547] [INFO] Selected 29 target genomes.
[2023-06-13 00:10:43,548] [INFO] Target genome list was writen to GCA_022720955.1_ASM2272095v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:10:43,563] [INFO] Task started: fastANI
[2023-06-13 00:10:43,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg63b729ea-5469-4ba0-81b9-c331aeadc846/GCA_022720955.1_ASM2272095v1_genomic.fna.gz --refList GCA_022720955.1_ASM2272095v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022720955.1_ASM2272095v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:10:55,909] [INFO] Task succeeded: fastANI
[2023-06-13 00:10:55,936] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 00:10:55,937] [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_015560765.1	s__Collinsella aerofaciens_M	95.9815	596	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1158	96.04	95.15	0.86	0.78	15	conclusive
GCA_008671135.1	s__Collinsella aerofaciens_J	94.8271	574	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2147	97.21	95.28	0.90	0.82	6	-
GCA_905215755.1	s__Collinsella sp905215755	94.7306	527	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0833	N/A	N/A	N/A	N/A	1	-
GCA_900541235.1	s__Collinsella sp900541235	94.6274	572	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.02	95.02	0.86	0.86	2	-
GCA_900544865.1	s__Collinsella sp900544865	94.614	546	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544465.1	s__Collinsella sp900544465	94.5662	430	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0579	100.00	100.00	0.98	0.98	2	-
GCA_900540895.1	s__Collinsella sp900540895	94.5466	573	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.25	0.87	0.87	2	-
GCA_900545505.1	s__Collinsella sp900545505	94.5398	371	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0349	N/A	N/A	N/A	N/A	1	-
GCA_900541135.1	s__Collinsella sp900541135	94.4861	560	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551365.1	s__Collinsella sp900551365	94.4815	492	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905197385.1	s__Collinsella sp905197385	94.4251	372	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554645.1	s__Collinsella sp900554645	94.3661	306	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900752475.1	s__Collinsella sp900752475	94.3637	405	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.66	99.66	0.82	0.82	2	-
GCF_003438495.1	s__Collinsella sp003438495	94.3501	577	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900541885.1	s__Collinsella sp900541885	94.3222	577	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900540995.1	s__Collinsella sp900540995	94.3134	549	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.96	99.96	0.96	0.96	2	-
GCA_900552755.1	s__Collinsella sp900552755	94.3007	434	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541025.1	s__Collinsella sp900541025	94.2141	555	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548515.1	s__Collinsella sp900548515	94.2141	488	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545615.1	s__Collinsella sp900545615	94.1737	521	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.94	99.94	0.92	0.92	2	-
GCA_900543605.1	s__Collinsella sp900543605	94.0955	532	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760245.1	s__Collinsella sp900760245	94.0922	477	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547765.1	s__Collinsella sp900547765	94.0009	545	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552295.1	s__Collinsella sp900552295	93.8972	383	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014871545.1	s__Collinsella sp014871545	93.8886	362	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0116	N/A	N/A	N/A	N/A	1	-
GCA_900545055.1	s__Collinsella sp900545055	93.7932	483	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553165.1	s__Collinsella sp900553165	93.6032	334	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761145.1	s__Collinsella sp900761145	93.14	505	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544225.1	s__Collinsella sp900544225	93.1277	472	674	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.82	95.63	0.93	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-13 00:10:55,940] [INFO] GTDB search result was written to GCA_022720955.1_ASM2272095v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:10:55,942] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:10:55,947] [INFO] DFAST_QC result json was written to GCA_022720955.1_ASM2272095v1_genomic.fna/dqc_result.json
[2023-06-13 00:10:55,947] [INFO] DFAST_QC completed!
[2023-06-13 00:10:55,947] [INFO] Total running time: 0h0m55s