[2023-06-05 18:50:43,275] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:50:43,287] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:50:43,287] [INFO] DQC Reference Directory: /var/lib/cwl/stgfec75afa-319f-4e02-93e7-64ebb325d46a/dqc_reference
[2023-06-05 18:50:44,781] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:50:44,789] [INFO] Task started: Prodigal
[2023-06-05 18:50:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg08d5629c-aaf1-4435-baca-eb7b030bf102/GCA_934868775.1_MTG244_bin.56.fa_genomic.fna.gz | prodigal -d GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/cds.fna -a GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:50:51,120] [INFO] Task succeeded: Prodigal
[2023-06-05 18:50:51,120] [INFO] Task started: HMMsearch
[2023-06-05 18:50:51,120] [INFO] Running command: hmmsearch --tblout GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfec75afa-319f-4e02-93e7-64ebb325d46a/dqc_reference/reference_markers.hmm GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:50:51,355] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:50:51,356] [INFO] Found 6/6 markers.
[2023-06-05 18:50:51,389] [INFO] Query marker FASTA was written to GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/markers.fasta
[2023-06-05 18:50:51,390] [INFO] Task started: Blastn
[2023-06-05 18:50:51,390] [INFO] Running command: blastn -query GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgfec75afa-319f-4e02-93e7-64ebb325d46a/dqc_reference/reference_markers.fasta -out GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:50:52,019] [INFO] Task succeeded: Blastn
[2023-06-05 18:50:52,022] [INFO] Selected 22 target genomes.
[2023-06-05 18:50:52,023] [INFO] Target genome list was writen to GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/target_genomes.txt
[2023-06-05 18:50:52,027] [INFO] Task started: fastANI
[2023-06-05 18:50:52,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg08d5629c-aaf1-4435-baca-eb7b030bf102/GCA_934868775.1_MTG244_bin.56.fa_genomic.fna.gz --refList GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/target_genomes.txt --output GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:51:07,095] [INFO] Task succeeded: fastANI
[2023-06-05 18:51:07,096] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfec75afa-319f-4e02-93e7-64ebb325d46a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:51:07,097] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfec75afa-319f-4e02-93e7-64ebb325d46a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:51:07,115] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:51:07,115] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:51:07,115] [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 fessum	strain=SNUG30386	GCA_003024715.1	2126740	2126740	type	True	77.0933	94	819	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.8398	151	819	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.7738	161	819	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.5192	87	819	95	below_threshold
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	76.5042	59	819	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	76.4766	63	819	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.4756	111	819	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.4601	110	819	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.4573	65	819	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.4502	113	819	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	76.4314	67	819	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.2514	54	819	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:51:07,117] [INFO] DFAST Taxonomy check result was written to GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/tc_result.tsv
[2023-06-05 18:51:07,118] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:51:07,118] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:51:07,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfec75afa-319f-4e02-93e7-64ebb325d46a/dqc_reference/checkm_data
[2023-06-05 18:51:07,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:51:07,185] [INFO] Task started: CheckM
[2023-06-05 18:51:07,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/checkm_input GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/checkm_result
[2023-06-05 18:51:32,156] [INFO] Task succeeded: CheckM
[2023-06-05 18:51:32,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:51:32,174] [INFO] ===== Completeness check finished =====
[2023-06-05 18:51:32,174] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:51:32,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/markers.fasta)
[2023-06-05 18:51:32,175] [INFO] Task started: Blastn
[2023-06-05 18:51:32,175] [INFO] Running command: blastn -query GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgfec75afa-319f-4e02-93e7-64ebb325d46a/dqc_reference/reference_markers_gtdb.fasta -out GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:51:33,248] [INFO] Task succeeded: Blastn
[2023-06-05 18:51:33,251] [INFO] Selected 16 target genomes.
[2023-06-05 18:51:33,251] [INFO] Target genome list was writen to GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:51:33,257] [INFO] Task started: fastANI
[2023-06-05 18:51:33,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg08d5629c-aaf1-4435-baca-eb7b030bf102/GCA_934868775.1_MTG244_bin.56.fa_genomic.fna.gz --refList GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:51:42,698] [INFO] Task succeeded: fastANI
[2023-06-05 18:51:42,708] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:51:42,708] [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_014385265.1	s__Copromonas sp000435795	96.7464	707	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.24	96.73	0.89	0.84	6	conclusive
GCA_905215775.1	s__Copromonas sp905215775	91.4665	668	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713185.1	s__Copromonas avistercoris	78.3902	243	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.24	98.19	0.97	0.95	4	-
GCA_018223415.1	s__Copromonas sp900541255	78.3164	316	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	99.81	99.68	0.96	0.93	4	-
GCA_910586315.1	s__Copromonas sp910586315	78.3117	245	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585355.1	s__Copromonas sp910585355	78.1465	248	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003480435.1	s__Copromonas sp900066055	77.9123	220	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.09	96.90	0.88	0.80	7	-
GCF_003435375.1	s__Copromonas sp900066535	77.8517	228	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	97.23	95.52	0.82	0.74	22	-
GCA_900549235.1	s__Enterocloster sp900549235	77.6938	129	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.03	99.00	0.79	0.77	3	-
GCA_900556965.1	s__Copromonas sp900556965	77.6046	113	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003478035.1	s__Copromonas sp900066785	77.5299	219	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	97.14	96.17	0.83	0.76	16	-
GCA_001304875.1	s__Ventrisoma faecale	77.2619	173	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrisoma	95.0	98.23	97.74	0.91	0.86	4	-
GCA_018715565.1	s__Ventrimonas merdavium	77.107	162	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.46	99.46	0.97	0.97	2	-
GCA_018380885.1	s__Enterocloster sp900555905	76.9768	169	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.89	98.89	0.95	0.95	2	-
GCA_019114845.1	s__Lachnoclostridium_A stercoripullorum	76.9598	164	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.44	98.44	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-06-05 18:51:42,711] [INFO] GTDB search result was written to GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 18:51:42,711] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:51:42,714] [INFO] DFAST_QC result json was written to GCA_934868775.1_MTG244_bin.56.fa_genomic.fna/dqc_result.json
[2023-06-05 18:51:42,715] [INFO] DFAST_QC completed!
[2023-06-05 18:51:42,715] [INFO] Total running time: 0h0m59s