[2024-01-24 14:03:07,850] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:07,853] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:07,853] [INFO] DQC Reference Directory: /var/lib/cwl/stg311d4a0f-13c0-4318-a0ed-882845b6abd1/dqc_reference
[2024-01-24 14:03:09,321] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:09,323] [INFO] Task started: Prodigal
[2024-01-24 14:03:09,323] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6be8d49-7d16-418b-9be0-2e0fe1aecf2c/GCF_000422285.1_ASM42228v1_genomic.fna.gz | prodigal -d GCF_000422285.1_ASM42228v1_genomic.fna/cds.fna -a GCF_000422285.1_ASM42228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:22,311] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:22,312] [INFO] Task started: HMMsearch
[2024-01-24 14:03:22,312] [INFO] Running command: hmmsearch --tblout GCF_000422285.1_ASM42228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg311d4a0f-13c0-4318-a0ed-882845b6abd1/dqc_reference/reference_markers.hmm GCF_000422285.1_ASM42228v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:22,675] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:22,677] [INFO] Found 6/6 markers.
[2024-01-24 14:03:22,714] [INFO] Query marker FASTA was written to GCF_000422285.1_ASM42228v1_genomic.fna/markers.fasta
[2024-01-24 14:03:22,714] [INFO] Task started: Blastn
[2024-01-24 14:03:22,714] [INFO] Running command: blastn -query GCF_000422285.1_ASM42228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg311d4a0f-13c0-4318-a0ed-882845b6abd1/dqc_reference/reference_markers.fasta -out GCF_000422285.1_ASM42228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:23,349] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:23,358] [INFO] Selected 19 target genomes.
[2024-01-24 14:03:23,358] [INFO] Target genome list was writen to GCF_000422285.1_ASM42228v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:23,371] [INFO] Task started: fastANI
[2024-01-24 14:03:23,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6be8d49-7d16-418b-9be0-2e0fe1aecf2c/GCF_000422285.1_ASM42228v1_genomic.fna.gz --refList GCF_000422285.1_ASM42228v1_genomic.fna/target_genomes.txt --output GCF_000422285.1_ASM42228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:38,891] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:38,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg311d4a0f-13c0-4318-a0ed-882845b6abd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:38,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg311d4a0f-13c0-4318-a0ed-882845b6abd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:38,898] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:38,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:38,899] [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
Desulfatiglans anilini	strain=DSM 4660	GCA_000422285.1	90728	90728	type	True	100.0	1494	1501	95	conclusive
Syntrophobacter fumaroxidans	strain=MPOB	GCA_000014965.1	119484	119484	type	True	84.0151	52	1501	95	below_threshold
Desulfarculus baarsii	strain=DSM 2075	GCA_000143965.1	453230	453230	type	True	82.2179	59	1501	95	below_threshold
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	75.9933	59	1501	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:38,901] [INFO] DFAST Taxonomy check result was written to GCF_000422285.1_ASM42228v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:38,901] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:38,902] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:38,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg311d4a0f-13c0-4318-a0ed-882845b6abd1/dqc_reference/checkm_data
[2024-01-24 14:03:38,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:38,952] [INFO] Task started: CheckM
[2024-01-24 14:03:38,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422285.1_ASM42228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422285.1_ASM42228v1_genomic.fna/checkm_input GCF_000422285.1_ASM42228v1_genomic.fna/checkm_result
[2024-01-24 14:04:19,244] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:19,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:19,265] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:19,265] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:19,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422285.1_ASM42228v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:19,266] [INFO] Task started: Blastn
[2024-01-24 14:04:19,266] [INFO] Running command: blastn -query GCF_000422285.1_ASM42228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg311d4a0f-13c0-4318-a0ed-882845b6abd1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422285.1_ASM42228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:20,119] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:20,123] [INFO] Selected 23 target genomes.
[2024-01-24 14:04:20,123] [INFO] Target genome list was writen to GCF_000422285.1_ASM42228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:20,211] [INFO] Task started: fastANI
[2024-01-24 14:04:20,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6be8d49-7d16-418b-9be0-2e0fe1aecf2c/GCF_000422285.1_ASM42228v1_genomic.fna.gz --refList GCF_000422285.1_ASM42228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422285.1_ASM42228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:36,080] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:36,094] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:36,094] [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_000422285.1	s__Desulfatiglans anilini	100.0	1494	1501	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__Desulfatiglans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900498135.1	s__Desulfatiglans sp900498135	94.1181	1260	1501	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__Desulfatiglans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840535.1	s__HGW-15 sp002840535	76.3266	71	1501	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__HGW-15;g__HGW-15	95.0	95.55	95.55	0.86	0.86	2	-
GCA_016926135.1	s__HGW-15 sp016926135	76.038	84	1501	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__HGW-15;g__HGW-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830135.1	s__JAHJTB01 sp018830135	75.6836	61	1501	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Adiutricales;f__JAHJTB01;g__JAHJTB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018812395.1	s__JAHJDS01 sp018812395	75.6074	52	1501	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__JAHJDS01;g__JAHJDS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016844935.1	s__NaphS2 sp016844935	75.4128	60	1501	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__NaphS2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:36,096] [INFO] GTDB search result was written to GCF_000422285.1_ASM42228v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:36,097] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:36,100] [INFO] DFAST_QC result json was written to GCF_000422285.1_ASM42228v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:36,100] [INFO] DFAST_QC completed!
[2024-01-24 14:04:36,100] [INFO] Total running time: 0h1m28s