[2023-06-05 18:56:29,166] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:56:29,168] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:56:29,168] [INFO] DQC Reference Directory: /var/lib/cwl/stge12fd2a0-bf70-4f4f-ae7d-6172bc42e803/dqc_reference
[2023-06-05 18:56:30,490] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:56:30,491] [INFO] Task started: Prodigal
[2023-06-05 18:56:30,491] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1431eee-657b-4db1-80dd-5cdb001960be/GCA_934835935.1_MTG223_bin.44.fa_genomic.fna.gz | prodigal -d GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/cds.fna -a GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:56:35,074] [INFO] Task succeeded: Prodigal
[2023-06-05 18:56:35,074] [INFO] Task started: HMMsearch
[2023-06-05 18:56:35,074] [INFO] Running command: hmmsearch --tblout GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge12fd2a0-bf70-4f4f-ae7d-6172bc42e803/dqc_reference/reference_markers.hmm GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:56:35,258] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:56:35,259] [INFO] Found 6/6 markers.
[2023-06-05 18:56:35,282] [INFO] Query marker FASTA was written to GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/markers.fasta
[2023-06-05 18:56:35,284] [INFO] Task started: Blastn
[2023-06-05 18:56:35,284] [INFO] Running command: blastn -query GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stge12fd2a0-bf70-4f4f-ae7d-6172bc42e803/dqc_reference/reference_markers.fasta -out GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:56:35,820] [INFO] Task succeeded: Blastn
[2023-06-05 18:56:35,823] [INFO] Selected 29 target genomes.
[2023-06-05 18:56:35,823] [INFO] Target genome list was writen to GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/target_genomes.txt
[2023-06-05 18:56:35,824] [INFO] Task started: fastANI
[2023-06-05 18:56:35,824] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1431eee-657b-4db1-80dd-5cdb001960be/GCA_934835935.1_MTG223_bin.44.fa_genomic.fna.gz --refList GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/target_genomes.txt --output GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:56:54,812] [INFO] Task succeeded: fastANI
[2023-06-05 18:56:54,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge12fd2a0-bf70-4f4f-ae7d-6172bc42e803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:56:54,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge12fd2a0-bf70-4f4f-ae7d-6172bc42e803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:56:54,819] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:56:54,820] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:56:54,820] [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	77.3103	50	453	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.6836	89	453	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.6317	93	453	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.3164	59	453	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.2933	51	453	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.1061	57	453	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.1024	57	453	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:56:54,822] [INFO] DFAST Taxonomy check result was written to GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/tc_result.tsv
[2023-06-05 18:56:54,822] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:56:54,822] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:56:54,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge12fd2a0-bf70-4f4f-ae7d-6172bc42e803/dqc_reference/checkm_data
[2023-06-05 18:56:54,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:56:54,849] [INFO] Task started: CheckM
[2023-06-05 18:56:54,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/checkm_input GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/checkm_result
[2023-06-05 18:57:12,707] [INFO] Task succeeded: CheckM
[2023-06-05 18:57:12,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:57:12,740] [INFO] ===== Completeness check finished =====
[2023-06-05 18:57:12,740] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:57:12,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/markers.fasta)
[2023-06-05 18:57:12,741] [INFO] Task started: Blastn
[2023-06-05 18:57:12,742] [INFO] Running command: blastn -query GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stge12fd2a0-bf70-4f4f-ae7d-6172bc42e803/dqc_reference/reference_markers_gtdb.fasta -out GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:13,631] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:13,642] [INFO] Selected 19 target genomes.
[2023-06-05 18:57:13,643] [INFO] Target genome list was writen to GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:57:13,648] [INFO] Task started: fastANI
[2023-06-05 18:57:13,648] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1431eee-657b-4db1-80dd-5cdb001960be/GCA_934835935.1_MTG223_bin.44.fa_genomic.fna.gz --refList GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:57:24,973] [INFO] Task succeeded: fastANI
[2023-06-05 18:57:24,985] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:57:24,985] [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	96.6925	418	453	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	91.5021	408	453	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_018223415.1	s__Copromonas sp900541255	78.1752	177	453	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	77.9934	138	453	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	77.971	140	453	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.24	98.19	0.97	0.95	4	-
GCF_003435375.1	s__Copromonas sp900066535	77.9099	124	453	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_910585355.1	s__Copromonas sp910585355	77.6483	136	453	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	77.5994	136	453	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_003478035.1	s__Copromonas sp900066785	77.2801	122	453	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_900556965.1	s__Copromonas sp900556965	77.2613	79	453	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_900549235.1	s__Enterocloster sp900549235	77.1548	60	453	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_018715565.1	s__Ventrimonas merdavium	76.9883	84	453	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_019114845.1	s__Lachnoclostridium_A stercoripullorum	76.8873	85	453	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	-
GCA_018380885.1	s__Enterocloster sp900555905	76.829	89	453	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_910585635.1	s__Caccovicinus sp910585635	76.6533	73	453	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160755.1	s__Lachnoclostridium_A sp002160755	76.6208	96	453	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.32	98.32	0.92	0.92	2	-
GCA_018223375.1	s__Clostridium_Q sp000435655	76.4743	72	453	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.36	96.90	0.90	0.85	8	-
GCF_000233455.1	s__Enterocloster citroniae	76.2118	54	453	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.23	99.13	0.87	0.84	10	-
--------------------------------------------------------------------------------
[2023-06-05 18:57:24,986] [INFO] GTDB search result was written to GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 18:57:24,987] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:57:24,990] [INFO] DFAST_QC result json was written to GCA_934835935.1_MTG223_bin.44.fa_genomic.fna/dqc_result.json
[2023-06-05 18:57:24,990] [INFO] DFAST_QC completed!
[2023-06-05 18:57:24,990] [INFO] Total running time: 0h0m56s