[2024-01-25 18:06:35,609] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:35,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:35,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f864c98-31be-4f0f-a7c4-0273afe39f70/dqc_reference
[2024-01-25 18:06:36,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:36,763] [INFO] Task started: Prodigal
[2024-01-25 18:06:36,763] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0be512c-c982-4abc-9420-efa08f26cef1/GCF_026013615.1_ASM2601361v1_genomic.fna.gz | prodigal -d GCF_026013615.1_ASM2601361v1_genomic.fna/cds.fna -a GCF_026013615.1_ASM2601361v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:55,366] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:55,366] [INFO] Task started: HMMsearch
[2024-01-25 18:06:55,366] [INFO] Running command: hmmsearch --tblout GCF_026013615.1_ASM2601361v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f864c98-31be-4f0f-a7c4-0273afe39f70/dqc_reference/reference_markers.hmm GCF_026013615.1_ASM2601361v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:55,673] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:55,675] [INFO] Found 6/6 markers.
[2024-01-25 18:06:55,716] [INFO] Query marker FASTA was written to GCF_026013615.1_ASM2601361v1_genomic.fna/markers.fasta
[2024-01-25 18:06:55,716] [INFO] Task started: Blastn
[2024-01-25 18:06:55,716] [INFO] Running command: blastn -query GCF_026013615.1_ASM2601361v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f864c98-31be-4f0f-a7c4-0273afe39f70/dqc_reference/reference_markers.fasta -out GCF_026013615.1_ASM2601361v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:56,266] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:56,269] [INFO] Selected 27 target genomes.
[2024-01-25 18:06:56,270] [INFO] Target genome list was writen to GCF_026013615.1_ASM2601361v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:56,313] [INFO] Task started: fastANI
[2024-01-25 18:06:56,313] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0be512c-c982-4abc-9420-efa08f26cef1/GCF_026013615.1_ASM2601361v1_genomic.fna.gz --refList GCF_026013615.1_ASM2601361v1_genomic.fna/target_genomes.txt --output GCF_026013615.1_ASM2601361v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:17,030] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:17,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f864c98-31be-4f0f-a7c4-0273afe39f70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:17,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f864c98-31be-4f0f-a7c4-0273afe39f70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:17,037] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:07:17,037] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:07:17,038] [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
Carboxylicivirga linearis	strain=FB218	GCA_018271995.1	1628157	1628157	type	True	79.0611	144	1808	95	below_threshold
Labilibacter marinus	strain=Y11	GCA_001659685.2	1477105	1477105	type	True	78.0073	229	1808	95	below_threshold
Saccharicrinis fermentans	strain=DSM 9555	GCA_000517085.1	982	982	type	True	77.9839	214	1808	95	below_threshold
Saccharicrinis fermentans	strain=JCM 21142	GCA_000583675.1	982	982	type	True	77.9804	205	1808	95	below_threshold
Labilibacter sediminis	strain=CG51	GCA_005877885.1	2570926	2570926	type	True	77.9075	295	1808	95	below_threshold
Saccharicrinis aurantiacus	strain=HQYD1	GCA_001660705.2	1849719	1849719	type	True	77.6366	167	1808	95	below_threshold
Marinifilum caeruleilacunae	strain=JC070	GCA_013141825.1	2499076	2499076	type	True	75.9371	55	1808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:17,039] [INFO] DFAST Taxonomy check result was written to GCF_026013615.1_ASM2601361v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:17,041] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:17,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:17,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f864c98-31be-4f0f-a7c4-0273afe39f70/dqc_reference/checkm_data
[2024-01-25 18:07:17,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:17,098] [INFO] Task started: CheckM
[2024-01-25 18:07:17,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026013615.1_ASM2601361v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026013615.1_ASM2601361v1_genomic.fna/checkm_input GCF_026013615.1_ASM2601361v1_genomic.fna/checkm_result
[2024-01-25 18:08:10,224] [INFO] Task succeeded: CheckM
[2024-01-25 18:08:10,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:08:10,239] [INFO] ===== Completeness check finished =====
[2024-01-25 18:08:10,240] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:08:10,241] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026013615.1_ASM2601361v1_genomic.fna/markers.fasta)
[2024-01-25 18:08:10,241] [INFO] Task started: Blastn
[2024-01-25 18:08:10,241] [INFO] Running command: blastn -query GCF_026013615.1_ASM2601361v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f864c98-31be-4f0f-a7c4-0273afe39f70/dqc_reference/reference_markers_gtdb.fasta -out GCF_026013615.1_ASM2601361v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:11,060] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:11,063] [INFO] Selected 27 target genomes.
[2024-01-25 18:08:11,063] [INFO] Target genome list was writen to GCF_026013615.1_ASM2601361v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:08:11,115] [INFO] Task started: fastANI
[2024-01-25 18:08:11,115] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0be512c-c982-4abc-9420-efa08f26cef1/GCF_026013615.1_ASM2601361v1_genomic.fna.gz --refList GCF_026013615.1_ASM2601361v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026013615.1_ASM2601361v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:08:28,544] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:28,550] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:08:28,550] [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_018271995.1	s__Carboxylicivirga linearis	79.0611	144	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001659685.2	s__Saccharicrinis marinus	78.0028	230	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000517085.1	s__Saccharicrinis fermentans	77.9839	214	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	99.97	99.97	1.00	1.00	2	-
GCF_005877885.1	s__Saccharicrinis sediminis	77.9107	294	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097485.1	s__Carboxylicivirga sp007097485	77.7883	97	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660705.2	s__Saccharicrinis aurantiacus	77.6159	168	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429115.1	s__Carboxylicivirga sp002429115	76.155	66	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016933045.1	s__Breznakibacter sp016933045	75.9245	66	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Breznakibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:08:28,551] [INFO] GTDB search result was written to GCF_026013615.1_ASM2601361v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:08:28,552] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:08:28,554] [INFO] DFAST_QC result json was written to GCF_026013615.1_ASM2601361v1_genomic.fna/dqc_result.json
[2024-01-25 18:08:28,554] [INFO] DFAST_QC completed!
[2024-01-25 18:08:28,554] [INFO] Total running time: 0h1m53s