[2023-06-04 20:05:49,165] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:05:49,170] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:05:49,170] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf2e3320-2d4d-4ad3-91a4-27e43cfd3098/dqc_reference
[2023-06-04 20:05:50,412] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:05:50,413] [INFO] Task started: Prodigal
[2023-06-04 20:05:50,413] [INFO] Running command: gunzip -c /var/lib/cwl/stgda0b3f3d-c9ee-43ab-90e8-073e554460d6/GCA_934643575.1_ERR7745561_bin.30_genomic.fna.gz | prodigal -d GCA_934643575.1_ERR7745561_bin.30_genomic.fna/cds.fna -a GCA_934643575.1_ERR7745561_bin.30_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:05:57,556] [INFO] Task succeeded: Prodigal
[2023-06-04 20:05:57,557] [INFO] Task started: HMMsearch
[2023-06-04 20:05:57,557] [INFO] Running command: hmmsearch --tblout GCA_934643575.1_ERR7745561_bin.30_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf2e3320-2d4d-4ad3-91a4-27e43cfd3098/dqc_reference/reference_markers.hmm GCA_934643575.1_ERR7745561_bin.30_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:05:57,815] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:05:57,816] [INFO] Found 6/6 markers.
[2023-06-04 20:05:57,843] [INFO] Query marker FASTA was written to GCA_934643575.1_ERR7745561_bin.30_genomic.fna/markers.fasta
[2023-06-04 20:05:57,843] [INFO] Task started: Blastn
[2023-06-04 20:05:57,843] [INFO] Running command: blastn -query GCA_934643575.1_ERR7745561_bin.30_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf2e3320-2d4d-4ad3-91a4-27e43cfd3098/dqc_reference/reference_markers.fasta -out GCA_934643575.1_ERR7745561_bin.30_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:05:58,585] [INFO] Task succeeded: Blastn
[2023-06-04 20:05:58,603] [INFO] Selected 15 target genomes.
[2023-06-04 20:05:58,604] [INFO] Target genome list was writen to GCA_934643575.1_ERR7745561_bin.30_genomic.fna/target_genomes.txt
[2023-06-04 20:05:58,607] [INFO] Task started: fastANI
[2023-06-04 20:05:58,607] [INFO] Running command: fastANI --query /var/lib/cwl/stgda0b3f3d-c9ee-43ab-90e8-073e554460d6/GCA_934643575.1_ERR7745561_bin.30_genomic.fna.gz --refList GCA_934643575.1_ERR7745561_bin.30_genomic.fna/target_genomes.txt --output GCA_934643575.1_ERR7745561_bin.30_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:06:05,746] [INFO] Task succeeded: fastANI
[2023-06-04 20:06:05,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf2e3320-2d4d-4ad3-91a4-27e43cfd3098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:06:05,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf2e3320-2d4d-4ad3-91a4-27e43cfd3098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:06:05,761] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:06:05,761] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 20:06:05,761] [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=ATCC 25986	GCA_000169035.1	74426	74426	type	True	91.4409	557	760	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	91.4335	561	760	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	91.4128	558	760	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.6638	227	760	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.7795	266	760	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.7362	273	760	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.6459	242	760	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.6123	233	760	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.4593	226	760	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.2813	238	760	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.903	218	760	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 20:06:05,763] [INFO] DFAST Taxonomy check result was written to GCA_934643575.1_ERR7745561_bin.30_genomic.fna/tc_result.tsv
[2023-06-04 20:06:05,764] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:06:05,764] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:06:05,764] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf2e3320-2d4d-4ad3-91a4-27e43cfd3098/dqc_reference/checkm_data
[2023-06-04 20:06:05,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:06:05,797] [INFO] Task started: CheckM
[2023-06-04 20:06:05,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934643575.1_ERR7745561_bin.30_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934643575.1_ERR7745561_bin.30_genomic.fna/checkm_input GCA_934643575.1_ERR7745561_bin.30_genomic.fna/checkm_result
[2023-06-04 20:06:31,908] [INFO] Task succeeded: CheckM
[2023-06-04 20:06:31,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:06:31,938] [INFO] ===== Completeness check finished =====
[2023-06-04 20:06:31,938] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:06:31,939] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934643575.1_ERR7745561_bin.30_genomic.fna/markers.fasta)
[2023-06-04 20:06:31,939] [INFO] Task started: Blastn
[2023-06-04 20:06:31,939] [INFO] Running command: blastn -query GCA_934643575.1_ERR7745561_bin.30_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf2e3320-2d4d-4ad3-91a4-27e43cfd3098/dqc_reference/reference_markers_gtdb.fasta -out GCA_934643575.1_ERR7745561_bin.30_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:06:33,320] [INFO] Task succeeded: Blastn
[2023-06-04 20:06:33,326] [INFO] Selected 29 target genomes.
[2023-06-04 20:06:33,327] [INFO] Target genome list was writen to GCA_934643575.1_ERR7745561_bin.30_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:06:33,384] [INFO] Task started: fastANI
[2023-06-04 20:06:33,384] [INFO] Running command: fastANI --query /var/lib/cwl/stgda0b3f3d-c9ee-43ab-90e8-073e554460d6/GCA_934643575.1_ERR7745561_bin.30_genomic.fna.gz --refList GCA_934643575.1_ERR7745561_bin.30_genomic.fna/target_genomes_gtdb.txt --output GCA_934643575.1_ERR7745561_bin.30_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:06:45,605] [INFO] Task succeeded: fastANI
[2023-06-04 20:06:45,632] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:06:45,632] [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_901212495.1	s__Collinsella aerofaciens_H	97.0569	640	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.63	95.88	0.84	0.79	16	conclusive
GCA_900767675.1	s__Collinsella sp900767675	93.2393	544	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754075.1	s__Collinsella sp900754075	93.0897	482	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.97	99.97	0.96	0.96	2	-
GCA_900756765.1	s__Collinsella sp900756765	93.0081	482	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905209765.1	s__Collinsella sp905209765	92.8147	458	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557505.1	s__Collinsella sp900557505	92.2953	289	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214105.1	s__Collinsella sp905214105	91.9737	572	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540095.1	s__Collinsella sp900540095	91.9582	453	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.82	99.82	0.89	0.89	2	-
GCA_900543615.1	s__Collinsella sp900543615	91.8128	469	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552685.1	s__Collinsella sp900552685	91.6684	308	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0737	N/A	N/A	N/A	N/A	1	-
GCA_900757465.1	s__Collinsella sp900757465	91.6467	440	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760905.1	s__Collinsella sp900760905	91.6415	510	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.28	95.28	0.83	0.83	2	-
GCA_900539035.1	s__Collinsella sp900539035	91.613	527	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.92	99.92	0.95	0.95	2	-
GCA_008668235.1	s__Collinsella aerofaciens_K	91.5926	503	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0357	97.54	95.17	0.89	0.81	5	-
GCA_900542125.1	s__Collinsella sp900542125	91.5608	532	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543605.1	s__Collinsella sp900543605	91.5346	496	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548495.1	s__Collinsella sp900548495	91.5126	484	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0367	N/A	N/A	N/A	N/A	1	-
GCA_900548515.1	s__Collinsella sp900548515	91.4906	479	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757505.1	s__Collinsella sp900757505	91.4842	475	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545905.1	s__Collinsella sp900545905	91.4285	386	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762015.1	s__Collinsella sp900762015	91.4259	460	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1172	N/A	N/A	N/A	N/A	1	-
GCA_900549025.1	s__Collinsella sp900549025	91.4222	468	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0692	97.49	95.13	0.83	0.77	3	-
GCA_900549085.1	s__Collinsella sp900549085	91.2169	507	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.95	99.95	0.97	0.97	2	-
GCA_900542825.1	s__Collinsella sp900542825	91.1344	527	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550785.1	s__Collinsella sp900550785	91.1212	448	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550205.1	s__Collinsella sp900550205	91.0202	405	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.03	95.54	0.85	0.78	4	-
GCA_900545505.1	s__Collinsella sp900545505	90.8728	344	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0349	N/A	N/A	N/A	N/A	1	-
GCA_900542085.1	s__Collinsella sp900542085	90.8175	534	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.96	0.96	2	-
GCA_900556205.1	s__Collinsella sp900556205	90.7851	301	760	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 20:06:45,636] [INFO] GTDB search result was written to GCA_934643575.1_ERR7745561_bin.30_genomic.fna/result_gtdb.tsv
[2023-06-04 20:06:45,637] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:06:45,641] [INFO] DFAST_QC result json was written to GCA_934643575.1_ERR7745561_bin.30_genomic.fna/dqc_result.json
[2023-06-04 20:06:45,642] [INFO] DFAST_QC completed!
[2023-06-04 20:06:45,642] [INFO] Total running time: 0h0m56s