[2024-01-24 11:06:04,655] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:06:04,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:06:04,658] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a300e17-f98c-4417-b7c1-38f66ce79b8a/dqc_reference
[2024-01-24 11:06:07,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:06:07,011] [INFO] Task started: Prodigal
[2024-01-24 11:06:07,012] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bc8613c-ac76-4a51-a3f3-060c69574650/GCF_007830715.1_ASM783071v1_genomic.fna.gz | prodigal -d GCF_007830715.1_ASM783071v1_genomic.fna/cds.fna -a GCF_007830715.1_ASM783071v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:25,973] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:25,974] [INFO] Task started: HMMsearch
[2024-01-24 11:06:25,974] [INFO] Running command: hmmsearch --tblout GCF_007830715.1_ASM783071v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a300e17-f98c-4417-b7c1-38f66ce79b8a/dqc_reference/reference_markers.hmm GCF_007830715.1_ASM783071v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:26,212] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:26,213] [INFO] Found 6/6 markers.
[2024-01-24 11:06:26,242] [INFO] Query marker FASTA was written to GCF_007830715.1_ASM783071v1_genomic.fna/markers.fasta
[2024-01-24 11:06:26,242] [INFO] Task started: Blastn
[2024-01-24 11:06:26,243] [INFO] Running command: blastn -query GCF_007830715.1_ASM783071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a300e17-f98c-4417-b7c1-38f66ce79b8a/dqc_reference/reference_markers.fasta -out GCF_007830715.1_ASM783071v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:26,847] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:26,851] [INFO] Selected 16 target genomes.
[2024-01-24 11:06:26,852] [INFO] Target genome list was writen to GCF_007830715.1_ASM783071v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:26,859] [INFO] Task started: fastANI
[2024-01-24 11:06:26,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bc8613c-ac76-4a51-a3f3-060c69574650/GCF_007830715.1_ASM783071v1_genomic.fna.gz --refList GCF_007830715.1_ASM783071v1_genomic.fna/target_genomes.txt --output GCF_007830715.1_ASM783071v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:38,491] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:38,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a300e17-f98c-4417-b7c1-38f66ce79b8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:38,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a300e17-f98c-4417-b7c1-38f66ce79b8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:38,505] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:06:38,505] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:38,505] [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 zoogleoformans	strain=ATCC 33285	GCA_007830715.1	28119	28119	type	True	100.0	1049	1051	95	conclusive
Bacteroides zoogleoformans	strain=ATCC 33285	GCA_002998435.1	28119	28119	type	True	99.9945	1051	1051	95	conclusive
Bacteroides heparinolyticus	strain=DSM 23917	GCA_004342845.1	28113	28113	type	True	88.9604	829	1051	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	79.7991	454	1051	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	79.7178	483	1051	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	79.6973	483	1051	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	79.6873	481	1051	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	79.5945	444	1051	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	79.1749	367	1051	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	79.041	326	1051	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	79.0207	328	1051	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	78.9395	350	1051	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	78.9183	357	1051	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	78.7543	332	1051	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	78.7359	329	1051	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	78.6264	313	1051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:38,507] [INFO] DFAST Taxonomy check result was written to GCF_007830715.1_ASM783071v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:38,507] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:38,507] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:38,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a300e17-f98c-4417-b7c1-38f66ce79b8a/dqc_reference/checkm_data
[2024-01-24 11:06:38,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:38,540] [INFO] Task started: CheckM
[2024-01-24 11:06:38,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830715.1_ASM783071v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830715.1_ASM783071v1_genomic.fna/checkm_input GCF_007830715.1_ASM783071v1_genomic.fna/checkm_result
[2024-01-24 11:07:32,558] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:32,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:32,577] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:32,577] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:32,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830715.1_ASM783071v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:32,578] [INFO] Task started: Blastn
[2024-01-24 11:07:32,578] [INFO] Running command: blastn -query GCF_007830715.1_ASM783071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a300e17-f98c-4417-b7c1-38f66ce79b8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830715.1_ASM783071v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:33,430] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:33,434] [INFO] Selected 15 target genomes.
[2024-01-24 11:07:33,434] [INFO] Target genome list was writen to GCF_007830715.1_ASM783071v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:33,448] [INFO] Task started: fastANI
[2024-01-24 11:07:33,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bc8613c-ac76-4a51-a3f3-060c69574650/GCF_007830715.1_ASM783071v1_genomic.fna.gz --refList GCF_007830715.1_ASM783071v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830715.1_ASM783071v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:45,549] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:45,566] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:45,566] [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_002998435.1	s__Bacteroides zoogleoformans	99.9945	1051	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_004342845.1	s__Bacteroides heparinolyticus	88.9772	827	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
GCF_000614125.1	s__Bacteroides rodentium	79.7671	468	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154205.1	s__Bacteroides uniformis	79.7286	482	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCF_004793475.1	s__Bacteroides sp002491635	79.4048	445	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	-
GCA_902388495.1	s__Bacteroides sp902388495	79.3731	388	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCA_905197435.1	s__Bacteroides sp905197435	79.2836	329	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578895.1	s__Bacteroides sp910578895	79.0734	332	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155815.1	s__Bacteroides eggerthii	79.041	326	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCF_003438615.1	s__Bacteroides sp003545565	79.0153	346	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_000374365.1	s__Bacteroides gallinarum	78.9183	357	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_900129655.1	s__Bacteroides clarus	78.7543	332	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCA_905203765.1	s__Bacteroides sp905203765	78.6117	297	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108345.1	s__Bacteroides ndongoniae	78.2648	290	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	97.32	0.85	0.83	4	-
GCA_900555635.1	s__Bacteroides sp900555635	77.7245	285	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.02	98.02	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:45,568] [INFO] GTDB search result was written to GCF_007830715.1_ASM783071v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:45,571] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:45,574] [INFO] DFAST_QC result json was written to GCF_007830715.1_ASM783071v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:45,575] [INFO] DFAST_QC completed!
[2024-01-24 11:07:45,575] [INFO] Total running time: 0h1m41s