[2024-01-25 18:43:35,566] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:35,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:35,568] [INFO] DQC Reference Directory: /var/lib/cwl/stg7463c237-994a-4f07-bbde-f6de09afe764/dqc_reference
[2024-01-25 18:43:36,664] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:36,665] [INFO] Task started: Prodigal
[2024-01-25 18:43:36,665] [INFO] Running command: gunzip -c /var/lib/cwl/stg35c4cc4a-471d-48c6-b7a9-724eda42e676/GCF_011044775.1_ASM1104477v1_genomic.fna.gz | prodigal -d GCF_011044775.1_ASM1104477v1_genomic.fna/cds.fna -a GCF_011044775.1_ASM1104477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:02,456] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:02,457] [INFO] Task started: HMMsearch
[2024-01-25 18:44:02,457] [INFO] Running command: hmmsearch --tblout GCF_011044775.1_ASM1104477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7463c237-994a-4f07-bbde-f6de09afe764/dqc_reference/reference_markers.hmm GCF_011044775.1_ASM1104477v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:02,663] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:02,664] [INFO] Found 6/6 markers.
[2024-01-25 18:44:02,691] [INFO] Query marker FASTA was written to GCF_011044775.1_ASM1104477v1_genomic.fna/markers.fasta
[2024-01-25 18:44:02,692] [INFO] Task started: Blastn
[2024-01-25 18:44:02,692] [INFO] Running command: blastn -query GCF_011044775.1_ASM1104477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7463c237-994a-4f07-bbde-f6de09afe764/dqc_reference/reference_markers.fasta -out GCF_011044775.1_ASM1104477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:03,298] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:03,301] [INFO] Selected 19 target genomes.
[2024-01-25 18:44:03,301] [INFO] Target genome list was writen to GCF_011044775.1_ASM1104477v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:03,327] [INFO] Task started: fastANI
[2024-01-25 18:44:03,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg35c4cc4a-471d-48c6-b7a9-724eda42e676/GCF_011044775.1_ASM1104477v1_genomic.fna.gz --refList GCF_011044775.1_ASM1104477v1_genomic.fna/target_genomes.txt --output GCF_011044775.1_ASM1104477v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:21,274] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:21,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7463c237-994a-4f07-bbde-f6de09afe764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:21,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7463c237-994a-4f07-bbde-f6de09afe764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:21,279] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:44:21,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:21,279] [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
Limisphaera ngatamarikiensis	strain=NGM72.4	GCA_011044775.1	1324935	1324935	type	True	100.0	1258	1260	95	conclusive
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	74.7785	65	1260	95	below_threshold
Embleya scabrispora	strain=DSM 41855	GCA_000372745.1	159449	159449	type	True	74.6159	62	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:21,280] [INFO] DFAST Taxonomy check result was written to GCF_011044775.1_ASM1104477v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:21,281] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:21,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:21,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7463c237-994a-4f07-bbde-f6de09afe764/dqc_reference/checkm_data
[2024-01-25 18:44:21,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:21,322] [INFO] Task started: CheckM
[2024-01-25 18:44:21,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011044775.1_ASM1104477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011044775.1_ASM1104477v1_genomic.fna/checkm_input GCF_011044775.1_ASM1104477v1_genomic.fna/checkm_result
[2024-01-25 18:45:40,762] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:40,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:40,783] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:40,784] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:40,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011044775.1_ASM1104477v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:40,785] [INFO] Task started: Blastn
[2024-01-25 18:45:40,785] [INFO] Running command: blastn -query GCF_011044775.1_ASM1104477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7463c237-994a-4f07-bbde-f6de09afe764/dqc_reference/reference_markers_gtdb.fasta -out GCF_011044775.1_ASM1104477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:41,902] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:41,905] [INFO] Selected 16 target genomes.
[2024-01-25 18:45:41,906] [INFO] Target genome list was writen to GCF_011044775.1_ASM1104477v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:41,923] [INFO] Task started: fastANI
[2024-01-25 18:45:41,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg35c4cc4a-471d-48c6-b7a9-724eda42e676/GCF_011044775.1_ASM1104477v1_genomic.fna.gz --refList GCF_011044775.1_ASM1104477v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011044775.1_ASM1104477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:56,040] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:56,054] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:56,054] [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_011044775.1	s__Limisphaera ngatamarikiensis	100.0	1258	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__NGM72-4;g__Limisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011058495.1	s__Limisphaera sp011058495	78.2981	486	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__NGM72-4;g__Limisphaera	95.0	99.99	99.98	0.99	0.99	4	-
GCA_015075445.1	s__DSVZ01 sp015075445	76.4179	117	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__DSVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716505.1	s__JADJWF01 sp016716505	76.4029	91	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__JADJWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695015.1	s__J093 sp003695015	76.265	106	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__J093	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011327785.1	s__DSVZ01 sp011327785	76.2609	139	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__DSVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002385705.1	s__UBA3939 sp002385705	76.0793	85	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA3939;g__UBA3939	95.0	99.95	99.95	0.96	0.96	2	-
GCA_903844265.1	s__CAIMTB01 sp903844265	76.0739	67	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__CAIMTB01;g__CAIMTB01	95.0	99.52	99.41	0.88	0.83	6	-
GCA_016935555.1	s__JAFGQR01 sp016935555	76.0343	108	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JAFGQR01;g__JAFGQR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860005.1	s__WYBW01 sp014860005	75.9278	99	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__WYBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873415.1	s__CAIQOK01 sp903873415	75.6857	59	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__CAIQOK01;g__CAIQOK01	95.0	99.92	99.92	0.92	0.92	2	-
GCA_009924135.1	s__SXTU01 sp009924135	75.6474	66	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138485.1	s__Palsa-1400 sp003138485	75.5859	65	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__Palsa-1400;g__Palsa-1400	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302195.1	s__UBA9464 sp017302195	75.3808	56	1260	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA9464	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:56,056] [INFO] GTDB search result was written to GCF_011044775.1_ASM1104477v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:56,056] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:56,059] [INFO] DFAST_QC result json was written to GCF_011044775.1_ASM1104477v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:56,059] [INFO] DFAST_QC completed!
[2024-01-25 18:45:56,059] [INFO] Total running time: 0h2m20s