[2024-01-25 19:59:05,651] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:05,655] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:05,656] [INFO] DQC Reference Directory: /var/lib/cwl/stg72e4a9c0-2eb4-462a-9019-3d026e3a58dc/dqc_reference
[2024-01-25 19:59:06,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:06,831] [INFO] Task started: Prodigal
[2024-01-25 19:59:06,831] [INFO] Running command: gunzip -c /var/lib/cwl/stg5523d389-409e-444b-a13c-603e7df498e0/GCF_001660705.2_ASM166070v2_genomic.fna.gz | prodigal -d GCF_001660705.2_ASM166070v2_genomic.fna/cds.fna -a GCF_001660705.2_ASM166070v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:23,403] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:23,403] [INFO] Task started: HMMsearch
[2024-01-25 19:59:23,403] [INFO] Running command: hmmsearch --tblout GCF_001660705.2_ASM166070v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72e4a9c0-2eb4-462a-9019-3d026e3a58dc/dqc_reference/reference_markers.hmm GCF_001660705.2_ASM166070v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:23,678] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:23,679] [INFO] Found 6/6 markers.
[2024-01-25 19:59:23,725] [INFO] Query marker FASTA was written to GCF_001660705.2_ASM166070v2_genomic.fna/markers.fasta
[2024-01-25 19:59:23,725] [INFO] Task started: Blastn
[2024-01-25 19:59:23,725] [INFO] Running command: blastn -query GCF_001660705.2_ASM166070v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg72e4a9c0-2eb4-462a-9019-3d026e3a58dc/dqc_reference/reference_markers.fasta -out GCF_001660705.2_ASM166070v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:24,296] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:24,299] [INFO] Selected 19 target genomes.
[2024-01-25 19:59:24,299] [INFO] Target genome list was writen to GCF_001660705.2_ASM166070v2_genomic.fna/target_genomes.txt
[2024-01-25 19:59:24,318] [INFO] Task started: fastANI
[2024-01-25 19:59:24,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg5523d389-409e-444b-a13c-603e7df498e0/GCF_001660705.2_ASM166070v2_genomic.fna.gz --refList GCF_001660705.2_ASM166070v2_genomic.fna/target_genomes.txt --output GCF_001660705.2_ASM166070v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:39,115] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:39,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72e4a9c0-2eb4-462a-9019-3d026e3a58dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:39,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72e4a9c0-2eb4-462a-9019-3d026e3a58dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:39,122] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:59:39,123] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:39,123] [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
Saccharicrinis aurantiacus	strain=HQYD1	GCA_001660705.2	1849719	1849719	type	True	100.0	1920	1924	95	conclusive
Labilibacter marinus	strain=Y11	GCA_001659685.2	1477105	1477105	type	True	78.0926	298	1924	95	below_threshold
Labilibacter sediminis	strain=CG51	GCA_005877885.1	2570926	2570926	type	True	77.8286	250	1924	95	below_threshold
Saccharicrinis fermentans	strain=DSM 9555	GCA_000517085.1	982	982	type	True	77.2998	169	1924	95	below_threshold
Saccharicrinis fermentans	strain=JCM 21142	GCA_000583675.1	982	982	type	True	77.2456	157	1924	95	below_threshold
Carboxylicivirga linearis	strain=FB218	GCA_018271995.1	1628157	1628157	type	True	76.9091	104	1924	95	below_threshold
Saccharicrinis carchari	strain=DSM 27040	GCA_900182605.1	1168039	1168039	type	True	76.8241	83	1924	95	below_threshold
Carboxylicivirga mesophila	strain=JCM 18290	GCA_018271975.1	1166478	1166478	type	True	76.0655	64	1924	95	below_threshold
Marinifilum flexuosum	strain=DSM 21950	GCA_003610555.1	1117708	1117708	type	True	75.5374	66	1924	95	below_threshold
Marinifilum fragile	strain=JCM 15579	GCA_001310955.1	570161	570161	type	True	75.4831	54	1924	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:39,124] [INFO] DFAST Taxonomy check result was written to GCF_001660705.2_ASM166070v2_genomic.fna/tc_result.tsv
[2024-01-25 19:59:39,124] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:39,125] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:39,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72e4a9c0-2eb4-462a-9019-3d026e3a58dc/dqc_reference/checkm_data
[2024-01-25 19:59:39,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:39,183] [INFO] Task started: CheckM
[2024-01-25 19:59:39,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001660705.2_ASM166070v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001660705.2_ASM166070v2_genomic.fna/checkm_input GCF_001660705.2_ASM166070v2_genomic.fna/checkm_result
[2024-01-25 20:00:26,991] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:26,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:27,009] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:27,009] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:27,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001660705.2_ASM166070v2_genomic.fna/markers.fasta)
[2024-01-25 20:00:27,011] [INFO] Task started: Blastn
[2024-01-25 20:00:27,011] [INFO] Running command: blastn -query GCF_001660705.2_ASM166070v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg72e4a9c0-2eb4-462a-9019-3d026e3a58dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_001660705.2_ASM166070v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:27,812] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:27,814] [INFO] Selected 17 target genomes.
[2024-01-25 20:00:27,814] [INFO] Target genome list was writen to GCF_001660705.2_ASM166070v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:27,834] [INFO] Task started: fastANI
[2024-01-25 20:00:27,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg5523d389-409e-444b-a13c-603e7df498e0/GCF_001660705.2_ASM166070v2_genomic.fna.gz --refList GCF_001660705.2_ASM166070v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001660705.2_ASM166070v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:41,696] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:41,703] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:41,703] [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_001660705.2	s__Saccharicrinis aurantiacus	100.0	1920	1924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001659685.2	s__Saccharicrinis marinus	78.0804	299	1924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005877885.1	s__Saccharicrinis sediminis	77.8704	247	1924	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	77.2998	169	1924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	99.97	99.97	1.00	1.00	2	-
GCF_018271995.1	s__Carboxylicivirga linearis	76.9327	103	1924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182605.1	s__Saccharicrinis carchari	76.8241	83	1924	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	76.1635	120	1924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610555.1	s__Marinifilum flexuosum	75.5125	65	1924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310955.1	s__Marinifilum fragile	75.4494	53	1924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:41,707] [INFO] GTDB search result was written to GCF_001660705.2_ASM166070v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:41,707] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:41,710] [INFO] DFAST_QC result json was written to GCF_001660705.2_ASM166070v2_genomic.fna/dqc_result.json
[2024-01-25 20:00:41,710] [INFO] DFAST_QC completed!
[2024-01-25 20:00:41,710] [INFO] Total running time: 0h1m36s