[2024-01-24 13:32:18,203] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:18,205] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:18,206] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1ffbbf0-9342-4540-b98c-dd117bed6bdf/dqc_reference
[2024-01-24 13:32:19,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:19,643] [INFO] Task started: Prodigal
[2024-01-24 13:32:19,643] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb4ddd9b-593f-474e-bebb-2480ac8c5fc4/GCF_007741515.1_ASM774151v1_genomic.fna.gz | prodigal -d GCF_007741515.1_ASM774151v1_genomic.fna/cds.fna -a GCF_007741515.1_ASM774151v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:38,557] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:38,557] [INFO] Task started: HMMsearch
[2024-01-24 13:32:38,558] [INFO] Running command: hmmsearch --tblout GCF_007741515.1_ASM774151v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1ffbbf0-9342-4540-b98c-dd117bed6bdf/dqc_reference/reference_markers.hmm GCF_007741515.1_ASM774151v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:38,901] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:38,902] [INFO] Found 6/6 markers.
[2024-01-24 13:32:38,954] [INFO] Query marker FASTA was written to GCF_007741515.1_ASM774151v1_genomic.fna/markers.fasta
[2024-01-24 13:32:38,957] [INFO] Task started: Blastn
[2024-01-24 13:32:38,958] [INFO] Running command: blastn -query GCF_007741515.1_ASM774151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1ffbbf0-9342-4540-b98c-dd117bed6bdf/dqc_reference/reference_markers.fasta -out GCF_007741515.1_ASM774151v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:39,569] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:39,572] [INFO] Selected 17 target genomes.
[2024-01-24 13:32:39,573] [INFO] Target genome list was writen to GCF_007741515.1_ASM774151v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:39,585] [INFO] Task started: fastANI
[2024-01-24 13:32:39,586] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb4ddd9b-593f-474e-bebb-2480ac8c5fc4/GCF_007741515.1_ASM774151v1_genomic.fna.gz --refList GCF_007741515.1_ASM774151v1_genomic.fna/target_genomes.txt --output GCF_007741515.1_ASM774151v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:56,080] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:56,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1ffbbf0-9342-4540-b98c-dd117bed6bdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:56,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1ffbbf0-9342-4540-b98c-dd117bed6bdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:56,090] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:56,091] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:56,091] [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
Adhaeretor mobilis	strain=HG15A2	GCA_007741515.1	1930276	1930276	type	True	100.0	1997	1998	95	conclusive
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	76.2893	73	1998	95	below_threshold
Aeoliella mucimassa	strain=Pan181	GCA_007748035.1	2527972	2527972	type	True	76.278	89	1998	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	76.0761	93	1998	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	76.0392	74	1998	95	below_threshold
Lignipirellula cremea	strain=Pla85_3_4	GCA_007751035.1	2528010	2528010	type	True	75.9956	50	1998	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.9774	133	1998	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.9422	108	1998	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.8376	95	1998	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:56,095] [INFO] DFAST Taxonomy check result was written to GCF_007741515.1_ASM774151v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:56,096] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:56,096] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:56,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1ffbbf0-9342-4540-b98c-dd117bed6bdf/dqc_reference/checkm_data
[2024-01-24 13:32:56,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:56,164] [INFO] Task started: CheckM
[2024-01-24 13:32:56,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007741515.1_ASM774151v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007741515.1_ASM774151v1_genomic.fna/checkm_input GCF_007741515.1_ASM774151v1_genomic.fna/checkm_result
[2024-01-24 13:33:49,934] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:49,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:49,957] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:49,957] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:49,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007741515.1_ASM774151v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:49,958] [INFO] Task started: Blastn
[2024-01-24 13:33:49,958] [INFO] Running command: blastn -query GCF_007741515.1_ASM774151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1ffbbf0-9342-4540-b98c-dd117bed6bdf/dqc_reference/reference_markers_gtdb.fasta -out GCF_007741515.1_ASM774151v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:50,762] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:50,767] [INFO] Selected 17 target genomes.
[2024-01-24 13:33:50,767] [INFO] Target genome list was writen to GCF_007741515.1_ASM774151v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:50,818] [INFO] Task started: fastANI
[2024-01-24 13:33:50,819] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb4ddd9b-593f-474e-bebb-2480ac8c5fc4/GCF_007741515.1_ASM774151v1_genomic.fna.gz --refList GCF_007741515.1_ASM774151v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007741515.1_ASM774151v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:05,852] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:05,872] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:05,872] [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_007741515.1	s__HG15A2 sp007741515	100.0	1997	1998	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__HG15A2	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013152515.1	s__Bythopirellula sp013152515	76.3225	58	1998	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702655.1	s__GCA-2702655 sp002702655	76.3022	141	1998	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__GCA-2702655	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859955.1	s__Botrimarina colliarenosi	76.2971	74	1998	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822725.1	s__Lacipirellula sp013822725	76.1275	100	1998	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007746075.1	s__Lacipirellula limnantheis	76.0772	93	1998	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	97.19	97.19	0.90	0.90	2	-
GCF_007753265.1	s__Botrimarina mediterranea	76.0688	74	1998	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	99.49	99.49	0.94	0.94	2	-
GCA_003576855.1	s__Lacipirellula sp003576855	75.9801	77	1998	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009177095.1	s__Lacipirellula parvula	75.9774	133	1998	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859765.1	s__Posidoniimonas corsicana	75.8508	94	1998	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:05,875] [INFO] GTDB search result was written to GCF_007741515.1_ASM774151v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:05,876] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:05,880] [INFO] DFAST_QC result json was written to GCF_007741515.1_ASM774151v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:05,881] [INFO] DFAST_QC completed!
[2024-01-24 13:34:05,881] [INFO] Total running time: 0h1m48s