[2023-06-29 05:38:32,722] [INFO] DFAST_QC pipeline started.
[2023-06-29 05:38:32,723] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 05:38:32,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a4940e7-47ac-4b4d-b12b-67a09ebd4a7e/dqc_reference
[2023-06-29 05:38:34,007] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 05:38:34,008] [INFO] Task started: Prodigal
[2023-06-29 05:38:34,008] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7653ecd-0e5b-49e7-81c7-fbf460849226/GCA_012273985.1_ASM1227398v1_genomic.fna.gz | prodigal -d GCA_012273985.1_ASM1227398v1_genomic.fna/cds.fna -a GCA_012273985.1_ASM1227398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 05:38:41,047] [INFO] Task succeeded: Prodigal
[2023-06-29 05:38:41,048] [INFO] Task started: HMMsearch
[2023-06-29 05:38:41,048] [INFO] Running command: hmmsearch --tblout GCA_012273985.1_ASM1227398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a4940e7-47ac-4b4d-b12b-67a09ebd4a7e/dqc_reference/reference_markers.hmm GCA_012273985.1_ASM1227398v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 05:38:41,278] [INFO] Task succeeded: HMMsearch
[2023-06-29 05:38:41,280] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc7653ecd-0e5b-49e7-81c7-fbf460849226/GCA_012273985.1_ASM1227398v1_genomic.fna.gz]
[2023-06-29 05:38:41,312] [INFO] Query marker FASTA was written to GCA_012273985.1_ASM1227398v1_genomic.fna/markers.fasta
[2023-06-29 05:38:41,312] [INFO] Task started: Blastn
[2023-06-29 05:38:41,312] [INFO] Running command: blastn -query GCA_012273985.1_ASM1227398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a4940e7-47ac-4b4d-b12b-67a09ebd4a7e/dqc_reference/reference_markers.fasta -out GCA_012273985.1_ASM1227398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:38:41,931] [INFO] Task succeeded: Blastn
[2023-06-29 05:38:41,936] [INFO] Selected 18 target genomes.
[2023-06-29 05:38:41,936] [INFO] Target genome list was writen to GCA_012273985.1_ASM1227398v1_genomic.fna/target_genomes.txt
[2023-06-29 05:38:41,940] [INFO] Task started: fastANI
[2023-06-29 05:38:41,940] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7653ecd-0e5b-49e7-81c7-fbf460849226/GCA_012273985.1_ASM1227398v1_genomic.fna.gz --refList GCA_012273985.1_ASM1227398v1_genomic.fna/target_genomes.txt --output GCA_012273985.1_ASM1227398v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 05:38:55,855] [INFO] Task succeeded: fastANI
[2023-06-29 05:38:55,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a4940e7-47ac-4b4d-b12b-67a09ebd4a7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 05:38:55,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a4940e7-47ac-4b4d-b12b-67a09ebd4a7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 05:38:55,859] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 05:38:55,859] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 05:38:55,859] [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
--------------------------------------------------------------------------------
[2023-06-29 05:38:55,861] [INFO] DFAST Taxonomy check result was written to GCA_012273985.1_ASM1227398v1_genomic.fna/tc_result.tsv
[2023-06-29 05:38:55,862] [INFO] ===== Taxonomy check completed =====
[2023-06-29 05:38:55,862] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 05:38:55,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a4940e7-47ac-4b4d-b12b-67a09ebd4a7e/dqc_reference/checkm_data
[2023-06-29 05:38:55,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 05:38:55,902] [INFO] Task started: CheckM
[2023-06-29 05:38:55,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012273985.1_ASM1227398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012273985.1_ASM1227398v1_genomic.fna/checkm_input GCA_012273985.1_ASM1227398v1_genomic.fna/checkm_result
[2023-06-29 05:39:21,983] [INFO] Task succeeded: CheckM
[2023-06-29 05:39:21,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 18.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 05:39:22,007] [INFO] ===== Completeness check finished =====
[2023-06-29 05:39:22,007] [INFO] ===== Start GTDB Search =====
[2023-06-29 05:39:22,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012273985.1_ASM1227398v1_genomic.fna/markers.fasta)
[2023-06-29 05:39:22,008] [INFO] Task started: Blastn
[2023-06-29 05:39:22,008] [INFO] Running command: blastn -query GCA_012273985.1_ASM1227398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a4940e7-47ac-4b4d-b12b-67a09ebd4a7e/dqc_reference/reference_markers_gtdb.fasta -out GCA_012273985.1_ASM1227398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:39:22,929] [INFO] Task succeeded: Blastn
[2023-06-29 05:39:22,934] [INFO] Selected 6 target genomes.
[2023-06-29 05:39:22,934] [INFO] Target genome list was writen to GCA_012273985.1_ASM1227398v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 05:39:22,938] [INFO] Task started: fastANI
[2023-06-29 05:39:22,938] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7653ecd-0e5b-49e7-81c7-fbf460849226/GCA_012273985.1_ASM1227398v1_genomic.fna.gz --refList GCA_012273985.1_ASM1227398v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012273985.1_ASM1227398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 05:39:28,536] [INFO] Task succeeded: fastANI
[2023-06-29 05:39:28,543] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 05:39:28,543] [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_017883205.1	s__JADGNZ01 sp017883205	86.6363	479	679	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__JADGNZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883235.1	s__JADGNZ01 sp017883235	79.802	331	679	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__JADGNZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247495.1	s__JADGNZ01 sp019247495	79.7169	290	679	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__JADGNZ01	95.0	99.75	99.65	0.94	0.93	3	-
GCA_019244185.1	s__QHVT01 sp019244185	77.8915	180	679	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVT01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_019242175.1	s__QHVT01 sp019242175	77.5472	133	679	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883215.1	s__QHVT01 sp017883215	77.4485	87	679	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 05:39:28,545] [INFO] GTDB search result was written to GCA_012273985.1_ASM1227398v1_genomic.fna/result_gtdb.tsv
[2023-06-29 05:39:28,546] [INFO] ===== GTDB Search completed =====
[2023-06-29 05:39:28,548] [INFO] DFAST_QC result json was written to GCA_012273985.1_ASM1227398v1_genomic.fna/dqc_result.json
[2023-06-29 05:39:28,548] [INFO] DFAST_QC completed!
[2023-06-29 05:39:28,548] [INFO] Total running time: 0h0m56s