[2023-06-13 13:31:50,045] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:31:50,050] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:31:50,050] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3ca7823-42e4-432d-9482-c48266000132/dqc_reference
[2023-06-13 13:31:51,324] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:31:51,324] [INFO] Task started: Prodigal
[2023-06-13 13:31:51,325] [INFO] Running command: gunzip -c /var/lib/cwl/stge69611dd-9972-4d4f-916c-21d45e7810e1/GCA_022742985.1_ASM2274298v1_genomic.fna.gz | prodigal -d GCA_022742985.1_ASM2274298v1_genomic.fna/cds.fna -a GCA_022742985.1_ASM2274298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:32:05,055] [INFO] Task succeeded: Prodigal
[2023-06-13 13:32:05,056] [INFO] Task started: HMMsearch
[2023-06-13 13:32:05,056] [INFO] Running command: hmmsearch --tblout GCA_022742985.1_ASM2274298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3ca7823-42e4-432d-9482-c48266000132/dqc_reference/reference_markers.hmm GCA_022742985.1_ASM2274298v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:32:05,312] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:32:05,314] [INFO] Found 6/6 markers.
[2023-06-13 13:32:05,364] [INFO] Query marker FASTA was written to GCA_022742985.1_ASM2274298v1_genomic.fna/markers.fasta
[2023-06-13 13:32:05,365] [INFO] Task started: Blastn
[2023-06-13 13:32:05,365] [INFO] Running command: blastn -query GCA_022742985.1_ASM2274298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3ca7823-42e4-432d-9482-c48266000132/dqc_reference/reference_markers.fasta -out GCA_022742985.1_ASM2274298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:32:06,018] [INFO] Task succeeded: Blastn
[2023-06-13 13:32:06,023] [INFO] Selected 24 target genomes.
[2023-06-13 13:32:06,023] [INFO] Target genome list was writen to GCA_022742985.1_ASM2274298v1_genomic.fna/target_genomes.txt
[2023-06-13 13:32:06,026] [INFO] Task started: fastANI
[2023-06-13 13:32:06,026] [INFO] Running command: fastANI --query /var/lib/cwl/stge69611dd-9972-4d4f-916c-21d45e7810e1/GCA_022742985.1_ASM2274298v1_genomic.fna.gz --refList GCA_022742985.1_ASM2274298v1_genomic.fna/target_genomes.txt --output GCA_022742985.1_ASM2274298v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:32:19,183] [INFO] Task succeeded: fastANI
[2023-06-13 13:32:19,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3ca7823-42e4-432d-9482-c48266000132/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:32:19,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3ca7823-42e4-432d-9482-c48266000132/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:32:19,191] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:32:19,191] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:32:19,191] [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
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	79.3515	174	535	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	78.025	57	535	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.8147	87	535	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.7816	88	535	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.7493	86	535	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.4739	82	535	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:32:19,195] [INFO] DFAST Taxonomy check result was written to GCA_022742985.1_ASM2274298v1_genomic.fna/tc_result.tsv
[2023-06-13 13:32:19,195] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:32:19,196] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:32:19,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3ca7823-42e4-432d-9482-c48266000132/dqc_reference/checkm_data
[2023-06-13 13:32:19,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:32:19,232] [INFO] Task started: CheckM
[2023-06-13 13:32:19,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022742985.1_ASM2274298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022742985.1_ASM2274298v1_genomic.fna/checkm_input GCA_022742985.1_ASM2274298v1_genomic.fna/checkm_result
[2023-06-13 13:33:01,009] [INFO] Task succeeded: CheckM
[2023-06-13 13:33:01,011] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 5.56%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 13:33:01,039] [INFO] ===== Completeness check finished =====
[2023-06-13 13:33:01,040] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:33:01,040] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022742985.1_ASM2274298v1_genomic.fna/markers.fasta)
[2023-06-13 13:33:01,040] [INFO] Task started: Blastn
[2023-06-13 13:33:01,041] [INFO] Running command: blastn -query GCA_022742985.1_ASM2274298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3ca7823-42e4-432d-9482-c48266000132/dqc_reference/reference_markers_gtdb.fasta -out GCA_022742985.1_ASM2274298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:33:01,855] [INFO] Task succeeded: Blastn
[2023-06-13 13:33:01,860] [INFO] Selected 9 target genomes.
[2023-06-13 13:33:01,860] [INFO] Target genome list was writen to GCA_022742985.1_ASM2274298v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:33:01,884] [INFO] Task started: fastANI
[2023-06-13 13:33:01,884] [INFO] Running command: fastANI --query /var/lib/cwl/stge69611dd-9972-4d4f-916c-21d45e7810e1/GCA_022742985.1_ASM2274298v1_genomic.fna.gz --refList GCA_022742985.1_ASM2274298v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022742985.1_ASM2274298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:33:06,611] [INFO] Task succeeded: fastANI
[2023-06-13 13:33:06,620] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 13:33:06,620] [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_900290275.1	s__Prevotella sp900290275	97.8616	508	535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.80	97.71	0.90	0.86	4	conclusive
GCA_900553155.1	s__Prevotella sp900553155	85.0272	303	535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
GCA_900546575.1	s__Prevotella sp900546575	80.5068	233	535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCA_900552515.1	s__Prevotella sp900552515	80.1423	211	535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.50	0.85	0.85	3	-
GCF_002265625.1	s__Prevotella sp002265625	80.1405	200	535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	-
GCA_900544495.1	s__Prevotella sp900544495	79.9609	242	535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_900550035.1	s__Prevotella sp900550035	79.9008	265	535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.93	0.97	0.97	3	-
GCF_019052365.1	s__Prevotella sp000434975	79.4808	171	535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCF_000235885.1	s__Prevotella stercorea	79.3389	174	535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.02	96.84	0.81	0.69	8	-
--------------------------------------------------------------------------------
[2023-06-13 13:33:06,622] [INFO] GTDB search result was written to GCA_022742985.1_ASM2274298v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:33:06,622] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:33:06,626] [INFO] DFAST_QC result json was written to GCA_022742985.1_ASM2274298v1_genomic.fna/dqc_result.json
[2023-06-13 13:33:06,626] [INFO] DFAST_QC completed!
[2023-06-13 13:33:06,626] [INFO] Total running time: 0h1m17s