[2023-06-29 13:14:23,914] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:14:23,917] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:14:23,917] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ca33ae9-85b3-4a56-a3f7-623fe32279cd/dqc_reference
[2023-06-29 13:14:25,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:14:25,189] [INFO] Task started: Prodigal
[2023-06-29 13:14:25,190] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f0eaca8-5ef3-4fb0-9c6c-88376dda5c70/GCA_023708685.1_ASM2370868v1_genomic.fna.gz | prodigal -d GCA_023708685.1_ASM2370868v1_genomic.fna/cds.fna -a GCA_023708685.1_ASM2370868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:14:46,806] [INFO] Task succeeded: Prodigal
[2023-06-29 13:14:46,806] [INFO] Task started: HMMsearch
[2023-06-29 13:14:46,807] [INFO] Running command: hmmsearch --tblout GCA_023708685.1_ASM2370868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ca33ae9-85b3-4a56-a3f7-623fe32279cd/dqc_reference/reference_markers.hmm GCA_023708685.1_ASM2370868v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:14:47,023] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:14:47,025] [INFO] Found 6/6 markers.
[2023-06-29 13:14:47,058] [INFO] Query marker FASTA was written to GCA_023708685.1_ASM2370868v1_genomic.fna/markers.fasta
[2023-06-29 13:14:47,058] [INFO] Task started: Blastn
[2023-06-29 13:14:47,058] [INFO] Running command: blastn -query GCA_023708685.1_ASM2370868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ca33ae9-85b3-4a56-a3f7-623fe32279cd/dqc_reference/reference_markers.fasta -out GCA_023708685.1_ASM2370868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:14:47,666] [INFO] Task succeeded: Blastn
[2023-06-29 13:14:47,670] [INFO] Selected 11 target genomes.
[2023-06-29 13:14:47,671] [INFO] Target genome list was writen to GCA_023708685.1_ASM2370868v1_genomic.fna/target_genomes.txt
[2023-06-29 13:14:47,671] [INFO] Task started: fastANI
[2023-06-29 13:14:47,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f0eaca8-5ef3-4fb0-9c6c-88376dda5c70/GCA_023708685.1_ASM2370868v1_genomic.fna.gz --refList GCA_023708685.1_ASM2370868v1_genomic.fna/target_genomes.txt --output GCA_023708685.1_ASM2370868v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:14:57,796] [INFO] Task succeeded: fastANI
[2023-06-29 13:14:57,797] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ca33ae9-85b3-4a56-a3f7-623fe32279cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:14:57,797] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ca33ae9-85b3-4a56-a3f7-623fe32279cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:14:57,806] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2023-06-29 13:14:57,806] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-29 13:14:57,807] [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 uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	98.8553	1103	1264	95	inconclusive
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	98.8109	1110	1264	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	98.7667	1101	1264	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	98.7529	1107	1264	95	inconclusive
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	96.0808	943	1264	95	inconclusive
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	94.7986	923	1264	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	92.2591	809	1264	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.3718	504	1264	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	80.2871	516	1264	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	79.4264	483	1264	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:14:57,809] [INFO] DFAST Taxonomy check result was written to GCA_023708685.1_ASM2370868v1_genomic.fna/tc_result.tsv
[2023-06-29 13:14:57,809] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:14:57,809] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:14:57,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ca33ae9-85b3-4a56-a3f7-623fe32279cd/dqc_reference/checkm_data
[2023-06-29 13:14:57,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:14:57,848] [INFO] Task started: CheckM
[2023-06-29 13:14:57,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708685.1_ASM2370868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708685.1_ASM2370868v1_genomic.fna/checkm_input GCA_023708685.1_ASM2370868v1_genomic.fna/checkm_result
[2023-06-29 13:15:57,722] [INFO] Task succeeded: CheckM
[2023-06-29 13:15:57,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:15:57,742] [INFO] ===== Completeness check finished =====
[2023-06-29 13:15:57,742] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:15:57,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708685.1_ASM2370868v1_genomic.fna/markers.fasta)
[2023-06-29 13:15:57,743] [INFO] Task started: Blastn
[2023-06-29 13:15:57,743] [INFO] Running command: blastn -query GCA_023708685.1_ASM2370868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ca33ae9-85b3-4a56-a3f7-623fe32279cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708685.1_ASM2370868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:15:58,597] [INFO] Task succeeded: Blastn
[2023-06-29 13:15:58,600] [INFO] Selected 14 target genomes.
[2023-06-29 13:15:58,600] [INFO] Target genome list was writen to GCA_023708685.1_ASM2370868v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:15:58,603] [INFO] Task started: fastANI
[2023-06-29 13:15:58,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f0eaca8-5ef3-4fb0-9c6c-88376dda5c70/GCA_023708685.1_ASM2370868v1_genomic.fna.gz --refList GCA_023708685.1_ASM2370868v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708685.1_ASM2370868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:16:08,895] [INFO] Task succeeded: fastANI
[2023-06-29 13:16:08,906] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:16:08,906] [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_000154205.1	s__Bacteroides uniformis	98.7747	1106	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	conclusive
GCF_000614125.1	s__Bacteroides rodentium	94.7986	923	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793475.1	s__Bacteroides sp002491635	91.9917	796	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	-
GCA_905197435.1	s__Bacteroides sp905197435	88.068	577	1264	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	81.6221	597	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCA_902388495.1	s__Bacteroides sp902388495	81.5674	637	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCA_905203765.1	s__Bacteroides sp905203765	81.2271	449	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129655.1	s__Bacteroides clarus	80.1817	489	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_000155815.1	s__Bacteroides eggerthii	80.1071	479	1264	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	80.1034	501	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_003438615.1	s__Bacteroides sp003545565	80.0515	502	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_000186225.1	s__Bacteroides helcogenes	79.6809	504	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905198575.1	s__Phocaeicola sp905198575	77.4355	76	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:16:08,909] [INFO] GTDB search result was written to GCA_023708685.1_ASM2370868v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:16:08,909] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:16:08,913] [INFO] DFAST_QC result json was written to GCA_023708685.1_ASM2370868v1_genomic.fna/dqc_result.json
[2023-06-29 13:16:08,913] [INFO] DFAST_QC completed!
[2023-06-29 13:16:08,913] [INFO] Total running time: 0h1m45s