[2023-06-18 10:25:30,070] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:25:30,074] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:25:30,074] [INFO] DQC Reference Directory: /var/lib/cwl/stg815881af-49ee-424e-917d-b18c96040f37/dqc_reference
[2023-06-18 10:25:31,400] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:25:31,401] [INFO] Task started: Prodigal
[2023-06-18 10:25:31,401] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b5c02d9-4c5a-42b9-81b4-82e97a37a78d/GCA_018653595.1_ASM1865359v1_genomic.fna.gz | prodigal -d GCA_018653595.1_ASM1865359v1_genomic.fna/cds.fna -a GCA_018653595.1_ASM1865359v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:25:39,267] [INFO] Task succeeded: Prodigal
[2023-06-18 10:25:39,267] [INFO] Task started: HMMsearch
[2023-06-18 10:25:39,268] [INFO] Running command: hmmsearch --tblout GCA_018653595.1_ASM1865359v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg815881af-49ee-424e-917d-b18c96040f37/dqc_reference/reference_markers.hmm GCA_018653595.1_ASM1865359v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:25:39,552] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:25:39,554] [INFO] Found 6/6 markers.
[2023-06-18 10:25:39,597] [INFO] Query marker FASTA was written to GCA_018653595.1_ASM1865359v1_genomic.fna/markers.fasta
[2023-06-18 10:25:39,598] [INFO] Task started: Blastn
[2023-06-18 10:25:39,598] [INFO] Running command: blastn -query GCA_018653595.1_ASM1865359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg815881af-49ee-424e-917d-b18c96040f37/dqc_reference/reference_markers.fasta -out GCA_018653595.1_ASM1865359v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:25:40,177] [INFO] Task succeeded: Blastn
[2023-06-18 10:25:40,182] [INFO] Selected 23 target genomes.
[2023-06-18 10:25:40,183] [INFO] Target genome list was writen to GCA_018653595.1_ASM1865359v1_genomic.fna/target_genomes.txt
[2023-06-18 10:25:40,192] [INFO] Task started: fastANI
[2023-06-18 10:25:40,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b5c02d9-4c5a-42b9-81b4-82e97a37a78d/GCA_018653595.1_ASM1865359v1_genomic.fna.gz --refList GCA_018653595.1_ASM1865359v1_genomic.fna/target_genomes.txt --output GCA_018653595.1_ASM1865359v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:25:54,790] [INFO] Task succeeded: fastANI
[2023-06-18 10:25:54,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg815881af-49ee-424e-917d-b18c96040f37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:25:54,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg815881af-49ee-424e-917d-b18c96040f37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:25:54,793] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 10:25:54,794] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 10:25:54,794] [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
--------------------------------------------------------------------------------
[2023-06-18 10:25:54,797] [INFO] DFAST Taxonomy check result was written to GCA_018653595.1_ASM1865359v1_genomic.fna/tc_result.tsv
[2023-06-18 10:25:54,799] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:25:54,799] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:25:54,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg815881af-49ee-424e-917d-b18c96040f37/dqc_reference/checkm_data
[2023-06-18 10:25:54,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:25:54,843] [INFO] Task started: CheckM
[2023-06-18 10:25:54,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018653595.1_ASM1865359v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018653595.1_ASM1865359v1_genomic.fna/checkm_input GCA_018653595.1_ASM1865359v1_genomic.fna/checkm_result
[2023-06-18 10:26:25,444] [INFO] Task succeeded: CheckM
[2023-06-18 10:26:25,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.59%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 10:26:25,482] [INFO] ===== Completeness check finished =====
[2023-06-18 10:26:25,483] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:26:25,483] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018653595.1_ASM1865359v1_genomic.fna/markers.fasta)
[2023-06-18 10:26:25,483] [INFO] Task started: Blastn
[2023-06-18 10:26:25,484] [INFO] Running command: blastn -query GCA_018653595.1_ASM1865359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg815881af-49ee-424e-917d-b18c96040f37/dqc_reference/reference_markers_gtdb.fasta -out GCA_018653595.1_ASM1865359v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:26:26,248] [INFO] Task succeeded: Blastn
[2023-06-18 10:26:26,254] [INFO] Selected 13 target genomes.
[2023-06-18 10:26:26,254] [INFO] Target genome list was writen to GCA_018653595.1_ASM1865359v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:26:26,285] [INFO] Task started: fastANI
[2023-06-18 10:26:26,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b5c02d9-4c5a-42b9-81b4-82e97a37a78d/GCA_018653595.1_ASM1865359v1_genomic.fna.gz --refList GCA_018653595.1_ASM1865359v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018653595.1_ASM1865359v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:26:34,753] [INFO] Task succeeded: fastANI
[2023-06-18 10:26:34,768] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 10:26:34,769] [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_018650795.1	s__JABMPR01 sp018650795	99.8906	967	1068	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.79	99.56	0.89	0.81	14	conclusive
GCA_018650445.1	s__JABMPR01 sp018650445	82.4119	617	1068	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.76	99.61	0.86	0.82	5	-
GCA_018673925.1	s__JABMPR01 sp018673925	81.1489	582	1068	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.95	99.91	0.96	0.94	16	-
GCA_016784025.1	s__JABMPR01 sp014382565	80.6751	589	1068	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.96	99.93	0.94	0.93	3	-
GCA_013202495.1	s__JABMPR01 sp013202495	80.4209	522	1068	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016784545.1	s__JABMPR01 sp016784545	79.9983	528	1068	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845065.1	s__JABMPR01 sp016845065	79.0811	440	1068	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016844945.1	s__JABMPR01 sp016844945	77.5667	253	1068	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 10:26:34,772] [INFO] GTDB search result was written to GCA_018653595.1_ASM1865359v1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:26:34,772] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:26:34,777] [INFO] DFAST_QC result json was written to GCA_018653595.1_ASM1865359v1_genomic.fna/dqc_result.json
[2023-06-18 10:26:34,777] [INFO] DFAST_QC completed!
[2023-06-18 10:26:34,777] [INFO] Total running time: 0h1m5s