[2023-06-28 16:53:34,516] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:53:34,518] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:53:34,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f3931d1-52bf-41c4-ba11-aa51d79eeef8/dqc_reference
[2023-06-28 16:53:35,721] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:53:35,722] [INFO] Task started: Prodigal
[2023-06-28 16:53:35,722] [INFO] Running command: gunzip -c /var/lib/cwl/stge7c8eded-9051-4061-8a74-2fc072e9d787/GCA_017480185.1_ASM1748018v1_genomic.fna.gz | prodigal -d GCA_017480185.1_ASM1748018v1_genomic.fna/cds.fna -a GCA_017480185.1_ASM1748018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:53:48,444] [INFO] Task succeeded: Prodigal
[2023-06-28 16:53:48,445] [INFO] Task started: HMMsearch
[2023-06-28 16:53:48,445] [INFO] Running command: hmmsearch --tblout GCA_017480185.1_ASM1748018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f3931d1-52bf-41c4-ba11-aa51d79eeef8/dqc_reference/reference_markers.hmm GCA_017480185.1_ASM1748018v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:53:48,692] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:53:48,694] [INFO] Found 6/6 markers.
[2023-06-28 16:53:48,717] [INFO] Query marker FASTA was written to GCA_017480185.1_ASM1748018v1_genomic.fna/markers.fasta
[2023-06-28 16:53:48,717] [INFO] Task started: Blastn
[2023-06-28 16:53:48,718] [INFO] Running command: blastn -query GCA_017480185.1_ASM1748018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f3931d1-52bf-41c4-ba11-aa51d79eeef8/dqc_reference/reference_markers.fasta -out GCA_017480185.1_ASM1748018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:53:49,311] [INFO] Task succeeded: Blastn
[2023-06-28 16:53:49,317] [INFO] Selected 28 target genomes.
[2023-06-28 16:53:49,317] [INFO] Target genome list was writen to GCA_017480185.1_ASM1748018v1_genomic.fna/target_genomes.txt
[2023-06-28 16:53:49,326] [INFO] Task started: fastANI
[2023-06-28 16:53:49,326] [INFO] Running command: fastANI --query /var/lib/cwl/stge7c8eded-9051-4061-8a74-2fc072e9d787/GCA_017480185.1_ASM1748018v1_genomic.fna.gz --refList GCA_017480185.1_ASM1748018v1_genomic.fna/target_genomes.txt --output GCA_017480185.1_ASM1748018v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:54:04,110] [INFO] Task succeeded: fastANI
[2023-06-28 16:54:04,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f3931d1-52bf-41c4-ba11-aa51d79eeef8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:54:04,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f3931d1-52bf-41c4-ba11-aa51d79eeef8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:54:04,113] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:54:04,113] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:54:04,113] [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
--------------------------------------------------------------------------------
[2023-06-28 16:54:04,115] [INFO] DFAST Taxonomy check result was written to GCA_017480185.1_ASM1748018v1_genomic.fna/tc_result.tsv
[2023-06-28 16:54:04,115] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:54:04,116] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:54:04,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f3931d1-52bf-41c4-ba11-aa51d79eeef8/dqc_reference/checkm_data
[2023-06-28 16:54:04,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:54:04,139] [INFO] Task started: CheckM
[2023-06-28 16:54:04,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017480185.1_ASM1748018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017480185.1_ASM1748018v1_genomic.fna/checkm_input GCA_017480185.1_ASM1748018v1_genomic.fna/checkm_result
[2023-06-28 16:54:43,766] [INFO] Task succeeded: CheckM
[2023-06-28 16:54:43,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:54:43,787] [INFO] ===== Completeness check finished =====
[2023-06-28 16:54:43,787] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:54:43,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017480185.1_ASM1748018v1_genomic.fna/markers.fasta)
[2023-06-28 16:54:43,788] [INFO] Task started: Blastn
[2023-06-28 16:54:43,788] [INFO] Running command: blastn -query GCA_017480185.1_ASM1748018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f3931d1-52bf-41c4-ba11-aa51d79eeef8/dqc_reference/reference_markers_gtdb.fasta -out GCA_017480185.1_ASM1748018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:54:44,588] [INFO] Task succeeded: Blastn
[2023-06-28 16:54:44,593] [INFO] Selected 31 target genomes.
[2023-06-28 16:54:44,593] [INFO] Target genome list was writen to GCA_017480185.1_ASM1748018v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:54:44,614] [INFO] Task started: fastANI
[2023-06-28 16:54:44,614] [INFO] Running command: fastANI --query /var/lib/cwl/stge7c8eded-9051-4061-8a74-2fc072e9d787/GCA_017480185.1_ASM1748018v1_genomic.fna.gz --refList GCA_017480185.1_ASM1748018v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017480185.1_ASM1748018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:54:56,665] [INFO] Task succeeded: fastANI
[2023-06-28 16:54:56,690] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:54:56,690] [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
GCA_017480185.1	s__UBA1711 sp017480185	100.0	592	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017479385.1	s__UBA1711 sp017479385	84.7529	97	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017480225.1	s__UBA1711 sp017480225	77.4982	66	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017501495.1	s__UBA1711 sp017501495	76.8993	55	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775135.1	s__UBA1711 sp902775135	76.8689	68	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800395.1	s__UBA1711 sp902800395	76.8367	60	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002349055.1	s__UBA1711 sp002349055	76.8156	71	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	99.90	99.90	0.97	0.97	2	-
GCA_017448185.1	s__UBA1711 sp017448185	76.8129	68	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551765.1	s__UBA1711 sp017551765	76.7945	58	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	96.72	96.72	0.78	0.78	2	-
GCA_017522105.1	s__UBA1711 sp017522105	76.6924	57	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017645585.1	s__UBA1711 sp017645585	76.674	53	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778925.1	s__UBA1711 sp902778925	76.5593	65	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.18	98.06	0.86	0.82	3	-
GCA_017480785.1	s__UBA1711 sp017480785	76.5456	69	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017455205.1	s__UBA1711 sp017455205	76.414	57	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017962545.1	s__UBA1711 sp017962545	76.3861	53	614	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:54:56,692] [INFO] GTDB search result was written to GCA_017480185.1_ASM1748018v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:54:56,692] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:54:56,695] [INFO] DFAST_QC result json was written to GCA_017480185.1_ASM1748018v1_genomic.fna/dqc_result.json
[2023-06-28 16:54:56,696] [INFO] DFAST_QC completed!
[2023-06-28 16:54:56,696] [INFO] Total running time: 0h1m22s