[2024-01-24 13:24:48,140] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:48,141] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:48,142] [INFO] DQC Reference Directory: /var/lib/cwl/stge13cd57d-ea84-41cc-8c31-40d6de027b28/dqc_reference
[2024-01-24 13:24:49,604] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:49,605] [INFO] Task started: Prodigal
[2024-01-24 13:24:49,605] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dd83147-24a7-4dd2-93ab-55dbfc78df33/GCF_007748155.1_ASM774815v1_genomic.fna.gz | prodigal -d GCF_007748155.1_ASM774815v1_genomic.fna/cds.fna -a GCF_007748155.1_ASM774815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:15,765] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:15,765] [INFO] Task started: HMMsearch
[2024-01-24 13:25:15,766] [INFO] Running command: hmmsearch --tblout GCF_007748155.1_ASM774815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge13cd57d-ea84-41cc-8c31-40d6de027b28/dqc_reference/reference_markers.hmm GCF_007748155.1_ASM774815v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:16,131] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:16,132] [INFO] Found 6/6 markers.
[2024-01-24 13:25:16,208] [INFO] Query marker FASTA was written to GCF_007748155.1_ASM774815v1_genomic.fna/markers.fasta
[2024-01-24 13:25:16,209] [INFO] Task started: Blastn
[2024-01-24 13:25:16,209] [INFO] Running command: blastn -query GCF_007748155.1_ASM774815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge13cd57d-ea84-41cc-8c31-40d6de027b28/dqc_reference/reference_markers.fasta -out GCF_007748155.1_ASM774815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:16,833] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:16,836] [INFO] Selected 18 target genomes.
[2024-01-24 13:25:16,836] [INFO] Target genome list was writen to GCF_007748155.1_ASM774815v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:16,847] [INFO] Task started: fastANI
[2024-01-24 13:25:16,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dd83147-24a7-4dd2-93ab-55dbfc78df33/GCF_007748155.1_ASM774815v1_genomic.fna.gz --refList GCF_007748155.1_ASM774815v1_genomic.fna/target_genomes.txt --output GCF_007748155.1_ASM774815v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:35,727] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:35,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge13cd57d-ea84-41cc-8c31-40d6de027b28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:35,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge13cd57d-ea84-41cc-8c31-40d6de027b28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:35,741] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:35,741] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:35,741] [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
Gimesia panareensis	strain=Enr10	GCA_007748155.1	2527978	2527978	type	True	100.0	2605	2609	95	conclusive
Gimesia benthica	strain=E7	GCA_009720525.1	2608982	2608982	type	True	83.4521	1887	2609	95	below_threshold
Gimesia chilikensis	strain=JC646	GCA_008329715.1	2605989	2605989	type	True	83.3786	1898	2609	95	below_threshold
Gimesia algae	strain=Pan161	GCA_007746795.1	2527971	2527971	type	True	78.8808	978	2609	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_000181475.1	122	122	type	True	78.7873	997	2609	95	below_threshold
Gimesia alba	strain=Pan241w	GCA_007744675.1	2527973	2527973	type	True	78.7775	1011	2609	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_008298035.1	122	122	type	True	78.7582	1021	2609	95	below_threshold
Gimesia fumaroli	strain=Enr17	GCA_007754425.1	2527976	2527976	type	True	78.5877	951	2609	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:35,743] [INFO] DFAST Taxonomy check result was written to GCF_007748155.1_ASM774815v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:35,744] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:35,744] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:35,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge13cd57d-ea84-41cc-8c31-40d6de027b28/dqc_reference/checkm_data
[2024-01-24 13:25:35,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:35,822] [INFO] Task started: CheckM
[2024-01-24 13:25:35,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007748155.1_ASM774815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007748155.1_ASM774815v1_genomic.fna/checkm_input GCF_007748155.1_ASM774815v1_genomic.fna/checkm_result
[2024-01-24 13:26:48,874] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:48,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:48,900] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:48,900] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:48,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007748155.1_ASM774815v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:48,901] [INFO] Task started: Blastn
[2024-01-24 13:26:48,901] [INFO] Running command: blastn -query GCF_007748155.1_ASM774815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge13cd57d-ea84-41cc-8c31-40d6de027b28/dqc_reference/reference_markers_gtdb.fasta -out GCF_007748155.1_ASM774815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:49,688] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:49,691] [INFO] Selected 8 target genomes.
[2024-01-24 13:26:49,691] [INFO] Target genome list was writen to GCF_007748155.1_ASM774815v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:49,709] [INFO] Task started: fastANI
[2024-01-24 13:26:49,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dd83147-24a7-4dd2-93ab-55dbfc78df33/GCF_007748155.1_ASM774815v1_genomic.fna.gz --refList GCF_007748155.1_ASM774815v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007748155.1_ASM774815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:03,810] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:03,817] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:03,818] [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_007748155.1	s__Gimesia panareensis	100.0	2604	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	96.61	95.86	0.91	0.90	3	conclusive
GCF_009720525.1	s__Gimesia benthica	83.4574	1885	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.18	95.18	0.86	0.86	2	-
GCF_008329715.1	s__Gimesia chilikensis	83.3762	1899	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.30	95.11	0.90	0.87	4	-
GCF_007746795.1	s__Gimesia algae	78.8836	978	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007744675.1	s__Gimesia alba	78.7727	1013	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008298035.1	s__Gimesia maris	78.7475	1023	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	98.48	97.03	0.94	0.89	7	-
GCA_002706765.1	s__Gimesia sp002706765	78.7166	1012	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	99.96	99.96	0.97	0.97	2	-
GCF_007754425.1	s__Gimesia fumaroli	78.5892	951	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:03,819] [INFO] GTDB search result was written to GCF_007748155.1_ASM774815v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:03,820] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:03,827] [INFO] DFAST_QC result json was written to GCF_007748155.1_ASM774815v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:03,828] [INFO] DFAST_QC completed!
[2024-01-24 13:27:03,828] [INFO] Total running time: 0h2m16s