[2024-01-25 19:58:50,730] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:50,731] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:50,731] [INFO] DQC Reference Directory: /var/lib/cwl/stg51b7ef69-6f0d-419b-98f3-729ed0f680fa/dqc_reference
[2024-01-25 19:58:51,933] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:51,934] [INFO] Task started: Prodigal
[2024-01-25 19:58:51,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg2398818e-95d9-47cb-b72d-ae3c7c9f6e23/GCF_025147325.1_ASM2514732v1_genomic.fna.gz | prodigal -d GCF_025147325.1_ASM2514732v1_genomic.fna/cds.fna -a GCF_025147325.1_ASM2514732v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:09,905] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:09,906] [INFO] Task started: HMMsearch
[2024-01-25 19:59:09,906] [INFO] Running command: hmmsearch --tblout GCF_025147325.1_ASM2514732v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51b7ef69-6f0d-419b-98f3-729ed0f680fa/dqc_reference/reference_markers.hmm GCF_025147325.1_ASM2514732v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:10,185] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:10,186] [INFO] Found 6/6 markers.
[2024-01-25 19:59:10,221] [INFO] Query marker FASTA was written to GCF_025147325.1_ASM2514732v1_genomic.fna/markers.fasta
[2024-01-25 19:59:10,222] [INFO] Task started: Blastn
[2024-01-25 19:59:10,222] [INFO] Running command: blastn -query GCF_025147325.1_ASM2514732v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51b7ef69-6f0d-419b-98f3-729ed0f680fa/dqc_reference/reference_markers.fasta -out GCF_025147325.1_ASM2514732v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:10,822] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:10,825] [INFO] Selected 14 target genomes.
[2024-01-25 19:59:10,826] [INFO] Target genome list was writen to GCF_025147325.1_ASM2514732v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:10,834] [INFO] Task started: fastANI
[2024-01-25 19:59:10,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg2398818e-95d9-47cb-b72d-ae3c7c9f6e23/GCF_025147325.1_ASM2514732v1_genomic.fna.gz --refList GCF_025147325.1_ASM2514732v1_genomic.fna/target_genomes.txt --output GCF_025147325.1_ASM2514732v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:22,626] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:22,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51b7ef69-6f0d-419b-98f3-729ed0f680fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:22,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51b7ef69-6f0d-419b-98f3-729ed0f680fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:22,634] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:59:22,634] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:22,635] [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 stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	100.0	1335	1335	95	conclusive
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	99.9919	1316	1335	95	conclusive
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	99.9513	1261	1335	95	conclusive
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	87.3661	849	1335	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	87.3025	844	1335	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	85.3795	782	1335	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	84.7937	813	1335	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	81.4048	608	1335	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	80.3879	525	1335	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	80.2506	360	1335	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:22,636] [INFO] DFAST Taxonomy check result was written to GCF_025147325.1_ASM2514732v1_genomic.fna/tc_result.tsv
[2024-01-25 19:59:22,636] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:22,636] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:22,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51b7ef69-6f0d-419b-98f3-729ed0f680fa/dqc_reference/checkm_data
[2024-01-25 19:59:22,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:22,677] [INFO] Task started: CheckM
[2024-01-25 19:59:22,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025147325.1_ASM2514732v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025147325.1_ASM2514732v1_genomic.fna/checkm_input GCF_025147325.1_ASM2514732v1_genomic.fna/checkm_result
[2024-01-25 20:00:12,348] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:12,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:12,366] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:12,366] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:12,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025147325.1_ASM2514732v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:12,367] [INFO] Task started: Blastn
[2024-01-25 20:00:12,367] [INFO] Running command: blastn -query GCF_025147325.1_ASM2514732v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51b7ef69-6f0d-419b-98f3-729ed0f680fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_025147325.1_ASM2514732v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:13,220] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:13,223] [INFO] Selected 13 target genomes.
[2024-01-25 20:00:13,223] [INFO] Target genome list was writen to GCF_025147325.1_ASM2514732v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:13,238] [INFO] Task started: fastANI
[2024-01-25 20:00:13,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg2398818e-95d9-47cb-b72d-ae3c7c9f6e23/GCF_025147325.1_ASM2514732v1_genomic.fna.gz --refList GCF_025147325.1_ASM2514732v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025147325.1_ASM2514732v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:23,593] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:23,599] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:23,599] [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_000154525.1	s__Bacteroides stercoris	99.9919	1316	1335	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	conclusive
GCF_900129655.1	s__Bacteroides clarus	87.3661	849	1335	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_003438615.1	s__Bacteroides sp003545565	85.4165	781	1335	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_000155815.1	s__Bacteroides eggerthii	84.6732	797	1335	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCA_910578895.1	s__Bacteroides sp910578895	83.9887	643	1335	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374365.1	s__Bacteroides gallinarum	83.7019	807	1335	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCA_905215345.1	s__Bacteroides sp905215345	80.0866	623	1335	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019129285.1	s__Bacteroides sp900552405	79.7015	479	1335	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.09	95.34	0.92	0.76	12	-
GCF_900106755.1	s__Bacteroides faecis	79.1312	308	1335	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:23,601] [INFO] GTDB search result was written to GCF_025147325.1_ASM2514732v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:23,602] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:23,605] [INFO] DFAST_QC result json was written to GCF_025147325.1_ASM2514732v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:23,605] [INFO] DFAST_QC completed!
[2024-01-25 20:00:23,605] [INFO] Total running time: 0h1m33s