[2023-06-30 21:46:15,399] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:46:15,401] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:46:15,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f316393-b3e2-470d-8ec2-3826505212aa/dqc_reference
[2023-06-30 21:46:16,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:46:16,607] [INFO] Task started: Prodigal
[2023-06-30 21:46:16,608] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e0f2e80-f329-4a47-8533-540a665a8cd9/GCA_016708765.1_ASM1670876v1_genomic.fna.gz | prodigal -d GCA_016708765.1_ASM1670876v1_genomic.fna/cds.fna -a GCA_016708765.1_ASM1670876v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:46:30,799] [INFO] Task succeeded: Prodigal
[2023-06-30 21:46:30,799] [INFO] Task started: HMMsearch
[2023-06-30 21:46:30,799] [INFO] Running command: hmmsearch --tblout GCA_016708765.1_ASM1670876v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f316393-b3e2-470d-8ec2-3826505212aa/dqc_reference/reference_markers.hmm GCA_016708765.1_ASM1670876v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:46:31,076] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:46:31,078] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9e0f2e80-f329-4a47-8533-540a665a8cd9/GCA_016708765.1_ASM1670876v1_genomic.fna.gz]
[2023-06-30 21:46:31,112] [INFO] Query marker FASTA was written to GCA_016708765.1_ASM1670876v1_genomic.fna/markers.fasta
[2023-06-30 21:46:31,113] [INFO] Task started: Blastn
[2023-06-30 21:46:31,113] [INFO] Running command: blastn -query GCA_016708765.1_ASM1670876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f316393-b3e2-470d-8ec2-3826505212aa/dqc_reference/reference_markers.fasta -out GCA_016708765.1_ASM1670876v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:46:31,685] [INFO] Task succeeded: Blastn
[2023-06-30 21:46:31,690] [INFO] Selected 25 target genomes.
[2023-06-30 21:46:31,691] [INFO] Target genome list was writen to GCA_016708765.1_ASM1670876v1_genomic.fna/target_genomes.txt
[2023-06-30 21:46:31,693] [INFO] Task started: fastANI
[2023-06-30 21:46:31,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e0f2e80-f329-4a47-8533-540a665a8cd9/GCA_016708765.1_ASM1670876v1_genomic.fna.gz --refList GCA_016708765.1_ASM1670876v1_genomic.fna/target_genomes.txt --output GCA_016708765.1_ASM1670876v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:46:51,925] [INFO] Task succeeded: fastANI
[2023-06-30 21:46:51,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f316393-b3e2-470d-8ec2-3826505212aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:46:51,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f316393-b3e2-470d-8ec2-3826505212aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:46:51,937] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:46:51,937] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 21:46:51,938] [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
Niabella hibiscisoli	strain=THG-DN5.5	GCA_022512515.1	1825928	1825928	type	True	76.7421	54	1171	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	76.3464	55	1171	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	76.314	71	1171	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	76.0979	68	1171	95	below_threshold
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	76.0246	58	1171	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	75.9402	53	1171	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 21:46:51,940] [INFO] DFAST Taxonomy check result was written to GCA_016708765.1_ASM1670876v1_genomic.fna/tc_result.tsv
[2023-06-30 21:46:51,940] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:46:51,940] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:46:51,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f316393-b3e2-470d-8ec2-3826505212aa/dqc_reference/checkm_data
[2023-06-30 21:46:51,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:46:51,980] [INFO] Task started: CheckM
[2023-06-30 21:46:51,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708765.1_ASM1670876v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708765.1_ASM1670876v1_genomic.fna/checkm_input GCA_016708765.1_ASM1670876v1_genomic.fna/checkm_result
[2023-06-30 21:47:35,615] [INFO] Task succeeded: CheckM
[2023-06-30 21:47:35,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 21:47:35,639] [INFO] ===== Completeness check finished =====
[2023-06-30 21:47:35,639] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:47:35,639] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708765.1_ASM1670876v1_genomic.fna/markers.fasta)
[2023-06-30 21:47:35,640] [INFO] Task started: Blastn
[2023-06-30 21:47:35,640] [INFO] Running command: blastn -query GCA_016708765.1_ASM1670876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f316393-b3e2-470d-8ec2-3826505212aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708765.1_ASM1670876v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:47:36,382] [INFO] Task succeeded: Blastn
[2023-06-30 21:47:36,387] [INFO] Selected 12 target genomes.
[2023-06-30 21:47:36,387] [INFO] Target genome list was writen to GCA_016708765.1_ASM1670876v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:47:36,388] [INFO] Task started: fastANI
[2023-06-30 21:47:36,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e0f2e80-f329-4a47-8533-540a665a8cd9/GCA_016708765.1_ASM1670876v1_genomic.fna.gz --refList GCA_016708765.1_ASM1670876v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708765.1_ASM1670876v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:47:45,169] [INFO] Task succeeded: fastANI
[2023-06-30 21:47:45,183] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:47:45,183] [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_016708765.1	s__JJ008 sp016708765	100.0	1170	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.32	99.14	0.92	0.90	6	conclusive
GCA_016706055.1	s__JJ008 sp016706055	86.7524	926	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.30	99.30	0.94	0.94	2	-
GCA_002127295.1	s__JJ008 sp002127295	78.0237	395	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719015.1	s__JJ008 sp016719015	77.7193	348	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.23	99.17	0.95	0.92	9	-
GCA_016719165.1	s__JJ008 sp016719165	77.5792	263	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	97.96	97.46	0.92	0.92	3	-
GCA_001464625.1	s__JJ008 sp001464625	77.5515	365	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786885.1	s__JJ008 sp016786885	77.1651	255	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720585.1	s__JJ008 sp016720585	77.0939	249	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	98.96	98.85	0.95	0.92	4	-
GCA_013140985.1	s__JJ008 sp013140985	77.0677	253	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331705.1	s__JJ008 sp011331705	77.0394	155	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002400415.1	s__JJ008 sp002400415	76.5832	179	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654695.1	s__VBAT01 sp015654695	76.4221	186	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__VBAT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 21:47:45,185] [INFO] GTDB search result was written to GCA_016708765.1_ASM1670876v1_genomic.fna/result_gtdb.tsv
[2023-06-30 21:47:45,185] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:47:45,189] [INFO] DFAST_QC result json was written to GCA_016708765.1_ASM1670876v1_genomic.fna/dqc_result.json
[2023-06-30 21:47:45,189] [INFO] DFAST_QC completed!
[2023-06-30 21:47:45,189] [INFO] Total running time: 0h1m30s