[2023-06-17 11:26:55,706] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:26:55,720] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:26:55,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d128850-4f0a-4de9-8d38-cdd64533ab06/dqc_reference
[2023-06-17 11:26:57,240] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:26:57,241] [INFO] Task started: Prodigal
[2023-06-17 11:26:57,242] [INFO] Running command: gunzip -c /var/lib/cwl/stgf205cb98-7731-48be-9e46-505bb9bdf3d8/GCA_028708055.1_ASM2870805v1_genomic.fna.gz | prodigal -d GCA_028708055.1_ASM2870805v1_genomic.fna/cds.fna -a GCA_028708055.1_ASM2870805v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:27:03,678] [INFO] Task succeeded: Prodigal
[2023-06-17 11:27:03,678] [INFO] Task started: HMMsearch
[2023-06-17 11:27:03,678] [INFO] Running command: hmmsearch --tblout GCA_028708055.1_ASM2870805v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d128850-4f0a-4de9-8d38-cdd64533ab06/dqc_reference/reference_markers.hmm GCA_028708055.1_ASM2870805v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:27:03,944] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:27:03,946] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf205cb98-7731-48be-9e46-505bb9bdf3d8/GCA_028708055.1_ASM2870805v1_genomic.fna.gz]
[2023-06-17 11:27:03,981] [INFO] Query marker FASTA was written to GCA_028708055.1_ASM2870805v1_genomic.fna/markers.fasta
[2023-06-17 11:27:03,981] [INFO] Task started: Blastn
[2023-06-17 11:27:03,981] [INFO] Running command: blastn -query GCA_028708055.1_ASM2870805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d128850-4f0a-4de9-8d38-cdd64533ab06/dqc_reference/reference_markers.fasta -out GCA_028708055.1_ASM2870805v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:27:04,529] [INFO] Task succeeded: Blastn
[2023-06-17 11:27:04,534] [INFO] Selected 6 target genomes.
[2023-06-17 11:27:04,535] [INFO] Target genome list was writen to GCA_028708055.1_ASM2870805v1_genomic.fna/target_genomes.txt
[2023-06-17 11:27:04,561] [INFO] Task started: fastANI
[2023-06-17 11:27:04,561] [INFO] Running command: fastANI --query /var/lib/cwl/stgf205cb98-7731-48be-9e46-505bb9bdf3d8/GCA_028708055.1_ASM2870805v1_genomic.fna.gz --refList GCA_028708055.1_ASM2870805v1_genomic.fna/target_genomes.txt --output GCA_028708055.1_ASM2870805v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:27:09,209] [INFO] Task succeeded: fastANI
[2023-06-17 11:27:09,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d128850-4f0a-4de9-8d38-cdd64533ab06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:27:09,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d128850-4f0a-4de9-8d38-cdd64533ab06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:27:09,212] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:27:09,212] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 11:27:09,212] [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
--------------------------------------------------------------------------------
[2023-06-17 11:27:09,215] [INFO] DFAST Taxonomy check result was written to GCA_028708055.1_ASM2870805v1_genomic.fna/tc_result.tsv
[2023-06-17 11:27:09,216] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:27:09,216] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:27:09,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d128850-4f0a-4de9-8d38-cdd64533ab06/dqc_reference/checkm_data
[2023-06-17 11:27:09,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:27:09,255] [INFO] Task started: CheckM
[2023-06-17 11:27:09,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708055.1_ASM2870805v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708055.1_ASM2870805v1_genomic.fna/checkm_input GCA_028708055.1_ASM2870805v1_genomic.fna/checkm_result
[2023-06-17 11:27:34,825] [INFO] Task succeeded: CheckM
[2023-06-17 11:27:34,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.11%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 11:27:34,851] [INFO] ===== Completeness check finished =====
[2023-06-17 11:27:34,852] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:27:34,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708055.1_ASM2870805v1_genomic.fna/markers.fasta)
[2023-06-17 11:27:34,853] [INFO] Task started: Blastn
[2023-06-17 11:27:34,853] [INFO] Running command: blastn -query GCA_028708055.1_ASM2870805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d128850-4f0a-4de9-8d38-cdd64533ab06/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708055.1_ASM2870805v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:27:35,458] [INFO] Task succeeded: Blastn
[2023-06-17 11:27:35,462] [INFO] Selected 11 target genomes.
[2023-06-17 11:27:35,462] [INFO] Target genome list was writen to GCA_028708055.1_ASM2870805v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:27:35,468] [INFO] Task started: fastANI
[2023-06-17 11:27:35,469] [INFO] Running command: fastANI --query /var/lib/cwl/stgf205cb98-7731-48be-9e46-505bb9bdf3d8/GCA_028708055.1_ASM2870805v1_genomic.fna.gz --refList GCA_028708055.1_ASM2870805v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708055.1_ASM2870805v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:27:40,037] [INFO] Task succeeded: fastANI
[2023-06-17 11:27:40,052] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 11:27:40,052] [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_002067705.1	s__Methanothrix sp002067705	84.6186	477	771	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391755.1	s__Methanothrix sp011391755	80.2296	179	771	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016927055.1	s__Methanothrix sp016927055	79.7054	300	771	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256595.1	s__Methanothrix sp002256595	78.7506	144	771	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	98.21	98.21	0.89	0.89	2	-
GCA_017994055.1	s__Methanothrix sp017994055	78.2427	179	771	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902385025.1	s__Methanothrix sp902385025	78.1694	135	771	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871465.1	s__Methanothrix sp903871465	78.1138	217	771	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	99.90	99.77	0.96	0.93	9	-
GCA_018052825.1	s__Methanothrix sp018052825	78.1088	167	771	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003857025.1	s__Methanothrix sp003857025	77.9542	171	771	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016706325.1	s__Methanothrix sp016706325	77.7168	139	771	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	98.78	98.75	0.93	0.92	4	-
GCA_002067365.1	s__Methanothrix sp002067365	77.3117	126	771	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:27:40,055] [INFO] GTDB search result was written to GCA_028708055.1_ASM2870805v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:27:40,055] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:27:40,058] [INFO] DFAST_QC result json was written to GCA_028708055.1_ASM2870805v1_genomic.fna/dqc_result.json
[2023-06-17 11:27:40,058] [INFO] DFAST_QC completed!
[2023-06-17 11:27:40,058] [INFO] Total running time: 0h0m44s