[2023-06-28 00:27:48,704] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:27:48,707] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:27:48,707] [INFO] DQC Reference Directory: /var/lib/cwl/stg40f0ccde-4d2d-407d-bf78-ee55998e3aef/dqc_reference
[2023-06-28 00:27:49,952] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:27:49,953] [INFO] Task started: Prodigal
[2023-06-28 00:27:49,954] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ac7146f-84e4-4f5b-8b13-9ffc94de305a/GCA_944321425.1_E10_bin247_genomic.fna.gz | prodigal -d GCA_944321425.1_E10_bin247_genomic.fna/cds.fna -a GCA_944321425.1_E10_bin247_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:28:06,535] [INFO] Task succeeded: Prodigal
[2023-06-28 00:28:06,535] [INFO] Task started: HMMsearch
[2023-06-28 00:28:06,535] [INFO] Running command: hmmsearch --tblout GCA_944321425.1_E10_bin247_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40f0ccde-4d2d-407d-bf78-ee55998e3aef/dqc_reference/reference_markers.hmm GCA_944321425.1_E10_bin247_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:28:06,797] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:28:06,798] [INFO] Found 6/6 markers.
[2023-06-28 00:28:06,830] [INFO] Query marker FASTA was written to GCA_944321425.1_E10_bin247_genomic.fna/markers.fasta
[2023-06-28 00:28:06,831] [INFO] Task started: Blastn
[2023-06-28 00:28:06,831] [INFO] Running command: blastn -query GCA_944321425.1_E10_bin247_genomic.fna/markers.fasta -db /var/lib/cwl/stg40f0ccde-4d2d-407d-bf78-ee55998e3aef/dqc_reference/reference_markers.fasta -out GCA_944321425.1_E10_bin247_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:28:07,442] [INFO] Task succeeded: Blastn
[2023-06-28 00:28:07,447] [INFO] Selected 16 target genomes.
[2023-06-28 00:28:07,448] [INFO] Target genome list was writen to GCA_944321425.1_E10_bin247_genomic.fna/target_genomes.txt
[2023-06-28 00:28:07,450] [INFO] Task started: fastANI
[2023-06-28 00:28:07,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ac7146f-84e4-4f5b-8b13-9ffc94de305a/GCA_944321425.1_E10_bin247_genomic.fna.gz --refList GCA_944321425.1_E10_bin247_genomic.fna/target_genomes.txt --output GCA_944321425.1_E10_bin247_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:28:19,527] [INFO] Task succeeded: fastANI
[2023-06-28 00:28:19,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40f0ccde-4d2d-407d-bf78-ee55998e3aef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:28:19,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40f0ccde-4d2d-407d-bf78-ee55998e3aef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:28:19,549] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2023-06-28 00:28:19,549] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 00:28:19,550] [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
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	98.5385	881	1053	95	conclusive
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	98.4963	891	1053	95	conclusive
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	87.4785	688	1053	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	87.3861	695	1053	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	87.2587	690	1053	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	84.7692	661	1053	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	84.7634	653	1053	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	84.7267	662	1053	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	83.8733	668	1053	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	83.7786	691	1053	95	below_threshold
Bacteroides luhongzhouii	strain=HF-5141	GCA_009193295.2	2650158	2650158	type	True	77.8663	224	1053	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_002959635.1	28116	28116	suspected-type	True	77.6677	228	1053	95	below_threshold
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	77.6249	223	1053	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	77.6207	228	1053	95	below_threshold
Bacteroides zhangwenhongii	strain=HF-5287	GCA_009193325.2	2650157	2650157	type	True	77.5861	224	1053	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 00:28:19,552] [INFO] DFAST Taxonomy check result was written to GCA_944321425.1_E10_bin247_genomic.fna/tc_result.tsv
[2023-06-28 00:28:19,552] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:28:19,552] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:28:19,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40f0ccde-4d2d-407d-bf78-ee55998e3aef/dqc_reference/checkm_data
[2023-06-28 00:28:19,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:28:19,590] [INFO] Task started: CheckM
[2023-06-28 00:28:19,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944321425.1_E10_bin247_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944321425.1_E10_bin247_genomic.fna/checkm_input GCA_944321425.1_E10_bin247_genomic.fna/checkm_result
[2023-06-28 00:29:07,919] [INFO] Task succeeded: CheckM
[2023-06-28 00:29:07,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:29:07,952] [INFO] ===== Completeness check finished =====
[2023-06-28 00:29:07,952] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:29:07,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944321425.1_E10_bin247_genomic.fna/markers.fasta)
[2023-06-28 00:29:07,953] [INFO] Task started: Blastn
[2023-06-28 00:29:07,953] [INFO] Running command: blastn -query GCA_944321425.1_E10_bin247_genomic.fna/markers.fasta -db /var/lib/cwl/stg40f0ccde-4d2d-407d-bf78-ee55998e3aef/dqc_reference/reference_markers_gtdb.fasta -out GCA_944321425.1_E10_bin247_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:29:08,851] [INFO] Task succeeded: Blastn
[2023-06-28 00:29:08,856] [INFO] Selected 14 target genomes.
[2023-06-28 00:29:08,857] [INFO] Target genome list was writen to GCA_944321425.1_E10_bin247_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:29:08,864] [INFO] Task started: fastANI
[2023-06-28 00:29:08,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ac7146f-84e4-4f5b-8b13-9ffc94de305a/GCA_944321425.1_E10_bin247_genomic.fna.gz --refList GCA_944321425.1_E10_bin247_genomic.fna/target_genomes_gtdb.txt --output GCA_944321425.1_E10_bin247_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:29:20,248] [INFO] Task succeeded: fastANI
[2023-06-28 00:29:20,265] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:29:20,265] [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_900129655.1	s__Bacteroides clarus	98.4963	891	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	conclusive
GCF_003438615.1	s__Bacteroides sp003545565	87.4156	690	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_000154525.1	s__Bacteroides stercoris	87.2711	689	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_000155815.1	s__Bacteroides eggerthii	84.7604	661	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCF_000374365.1	s__Bacteroides gallinarum	83.7862	690	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCA_910578895.1	s__Bacteroides sp910578895	83.4737	551	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195635.1	s__Bacteroides fluxus	79.4621	462	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCF_009193295.2	s__Bacteroides luhongzhouii	77.8411	224	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_014750685.1	s__Bacteroides sp014750685	77.7797	249	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	77.7218	230	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCA_902362375.1	s__Bacteroides sp902362375	77.7114	237	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_001314995.1	s__Bacteroides ovatus	77.604	230	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCF_009193325.2	s__Bacteroides zhangwenhongi	77.5861	224	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	-
--------------------------------------------------------------------------------
[2023-06-28 00:29:20,267] [INFO] GTDB search result was written to GCA_944321425.1_E10_bin247_genomic.fna/result_gtdb.tsv
[2023-06-28 00:29:20,268] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:29:20,271] [INFO] DFAST_QC result json was written to GCA_944321425.1_E10_bin247_genomic.fna/dqc_result.json
[2023-06-28 00:29:20,272] [INFO] DFAST_QC completed!
[2023-06-28 00:29:20,272] [INFO] Total running time: 0h1m32s