[2024-01-25 18:17:05,530] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:17:05,532] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:17:05,532] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1abee09-2f8e-42e2-9373-cf933d262ba4/dqc_reference
[2024-01-25 18:17:06,703] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:17:06,703] [INFO] Task started: Prodigal
[2024-01-25 18:17:06,704] [INFO] Running command: gunzip -c /var/lib/cwl/stgbce27ae7-0f12-4d66-8f62-32ca41cbe580/GCF_024704915.1_ASM2470491v1_genomic.fna.gz | prodigal -d GCF_024704915.1_ASM2470491v1_genomic.fna/cds.fna -a GCF_024704915.1_ASM2470491v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:17:26,136] [INFO] Task succeeded: Prodigal
[2024-01-25 18:17:26,137] [INFO] Task started: HMMsearch
[2024-01-25 18:17:26,137] [INFO] Running command: hmmsearch --tblout GCF_024704915.1_ASM2470491v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1abee09-2f8e-42e2-9373-cf933d262ba4/dqc_reference/reference_markers.hmm GCF_024704915.1_ASM2470491v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:17:26,419] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:17:26,420] [INFO] Found 6/6 markers.
[2024-01-25 18:17:26,458] [INFO] Query marker FASTA was written to GCF_024704915.1_ASM2470491v1_genomic.fna/markers.fasta
[2024-01-25 18:17:26,458] [INFO] Task started: Blastn
[2024-01-25 18:17:26,458] [INFO] Running command: blastn -query GCF_024704915.1_ASM2470491v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1abee09-2f8e-42e2-9373-cf933d262ba4/dqc_reference/reference_markers.fasta -out GCF_024704915.1_ASM2470491v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:27,024] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:27,028] [INFO] Selected 9 target genomes.
[2024-01-25 18:17:27,028] [INFO] Target genome list was writen to GCF_024704915.1_ASM2470491v1_genomic.fna/target_genomes.txt
[2024-01-25 18:17:27,036] [INFO] Task started: fastANI
[2024-01-25 18:17:27,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgbce27ae7-0f12-4d66-8f62-32ca41cbe580/GCF_024704915.1_ASM2470491v1_genomic.fna.gz --refList GCF_024704915.1_ASM2470491v1_genomic.fna/target_genomes.txt --output GCF_024704915.1_ASM2470491v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:17:35,483] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:35,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1abee09-2f8e-42e2-9373-cf933d262ba4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:17:35,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1abee09-2f8e-42e2-9373-cf933d262ba4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:17:35,491] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:17:35,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:17:35,492] [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 muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	100.0	1335	1342	95	conclusive
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	92.5165	898	1342	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	92.4564	919	1342	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	92.4408	916	1342	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	92.4399	913	1342	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	92.0106	885	1342	95	below_threshold
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	90.8611	874	1342	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.5257	506	1342	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	79.5968	464	1342	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:17:35,493] [INFO] DFAST Taxonomy check result was written to GCF_024704915.1_ASM2470491v1_genomic.fna/tc_result.tsv
[2024-01-25 18:17:35,494] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:17:35,494] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:17:35,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1abee09-2f8e-42e2-9373-cf933d262ba4/dqc_reference/checkm_data
[2024-01-25 18:17:35,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:17:35,538] [INFO] Task started: CheckM
[2024-01-25 18:17:35,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024704915.1_ASM2470491v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024704915.1_ASM2470491v1_genomic.fna/checkm_input GCF_024704915.1_ASM2470491v1_genomic.fna/checkm_result
[2024-01-25 18:18:29,128] [INFO] Task succeeded: CheckM
[2024-01-25 18:18:29,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:18:29,147] [INFO] ===== Completeness check finished =====
[2024-01-25 18:18:29,148] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:18:29,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024704915.1_ASM2470491v1_genomic.fna/markers.fasta)
[2024-01-25 18:18:29,149] [INFO] Task started: Blastn
[2024-01-25 18:18:29,149] [INFO] Running command: blastn -query GCF_024704915.1_ASM2470491v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1abee09-2f8e-42e2-9373-cf933d262ba4/dqc_reference/reference_markers_gtdb.fasta -out GCF_024704915.1_ASM2470491v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:18:29,958] [INFO] Task succeeded: Blastn
[2024-01-25 18:18:29,962] [INFO] Selected 11 target genomes.
[2024-01-25 18:18:29,962] [INFO] Target genome list was writen to GCF_024704915.1_ASM2470491v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:18:29,976] [INFO] Task started: fastANI
[2024-01-25 18:18:29,977] [INFO] Running command: fastANI --query /var/lib/cwl/stgbce27ae7-0f12-4d66-8f62-32ca41cbe580/GCF_024704915.1_ASM2470491v1_genomic.fna.gz --refList GCF_024704915.1_ASM2470491v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024704915.1_ASM2470491v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:18:38,883] [INFO] Task succeeded: fastANI
[2024-01-25 18:18:38,890] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:18:38,891] [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_004793475.1	s__Bacteroides sp002491635	98.1274	1087	1342	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	conclusive
GCF_000154205.1	s__Bacteroides uniformis	92.4417	917	1342	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCF_000614125.1	s__Bacteroides rodentium	90.8611	874	1342	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905197435.1	s__Bacteroides sp905197435	86.532	555	1342	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	81.6735	623	1342	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	81.3843	594	1342	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	80.5696	419	1342	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	80.2473	474	1342	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	80.0621	482	1342	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCF_004342845.1	s__Bacteroides heparinolyticus	79.8305	475	1342	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
GCF_000186225.1	s__Bacteroides helcogenes	79.8123	499	1342	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:18:38,892] [INFO] GTDB search result was written to GCF_024704915.1_ASM2470491v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:18:38,892] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:18:38,897] [INFO] DFAST_QC result json was written to GCF_024704915.1_ASM2470491v1_genomic.fna/dqc_result.json
[2024-01-25 18:18:38,898] [INFO] DFAST_QC completed!
[2024-01-25 18:18:38,898] [INFO] Total running time: 0h1m33s