[2023-06-05 01:18:29,201] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:18:29,204] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:18:29,204] [INFO] DQC Reference Directory: /var/lib/cwl/stg5493a14a-d764-4153-aec2-8fba42ff62ae/dqc_reference
[2023-06-05 01:18:30,613] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:18:30,614] [INFO] Task started: Prodigal
[2023-06-05 01:18:30,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg07ffa22e-44bb-4d4e-94c2-88ae2388fd94/GCA_934132995.1_ERR7746048_bin.75_genomic.fna.gz | prodigal -d GCA_934132995.1_ERR7746048_bin.75_genomic.fna/cds.fna -a GCA_934132995.1_ERR7746048_bin.75_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:18:32,571] [INFO] Task succeeded: Prodigal
[2023-06-05 01:18:32,571] [INFO] Task started: HMMsearch
[2023-06-05 01:18:32,571] [INFO] Running command: hmmsearch --tblout GCA_934132995.1_ERR7746048_bin.75_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5493a14a-d764-4153-aec2-8fba42ff62ae/dqc_reference/reference_markers.hmm GCA_934132995.1_ERR7746048_bin.75_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:18:32,838] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:18:32,839] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg07ffa22e-44bb-4d4e-94c2-88ae2388fd94/GCA_934132995.1_ERR7746048_bin.75_genomic.fna.gz]
[2023-06-05 01:18:32,858] [INFO] Query marker FASTA was written to GCA_934132995.1_ERR7746048_bin.75_genomic.fna/markers.fasta
[2023-06-05 01:18:32,858] [INFO] Task started: Blastn
[2023-06-05 01:18:32,859] [INFO] Running command: blastn -query GCA_934132995.1_ERR7746048_bin.75_genomic.fna/markers.fasta -db /var/lib/cwl/stg5493a14a-d764-4153-aec2-8fba42ff62ae/dqc_reference/reference_markers.fasta -out GCA_934132995.1_ERR7746048_bin.75_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:18:33,469] [INFO] Task succeeded: Blastn
[2023-06-05 01:18:33,474] [INFO] Selected 28 target genomes.
[2023-06-05 01:18:33,475] [INFO] Target genome list was writen to GCA_934132995.1_ERR7746048_bin.75_genomic.fna/target_genomes.txt
[2023-06-05 01:18:33,479] [INFO] Task started: fastANI
[2023-06-05 01:18:33,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg07ffa22e-44bb-4d4e-94c2-88ae2388fd94/GCA_934132995.1_ERR7746048_bin.75_genomic.fna.gz --refList GCA_934132995.1_ERR7746048_bin.75_genomic.fna/target_genomes.txt --output GCA_934132995.1_ERR7746048_bin.75_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:18:45,790] [INFO] Task succeeded: fastANI
[2023-06-05 01:18:45,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5493a14a-d764-4153-aec2-8fba42ff62ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:18:45,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5493a14a-d764-4153-aec2-8fba42ff62ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:18:45,793] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:18:45,793] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 01:18:45,793] [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
--------------------------------------------------------------------------------
[2023-06-05 01:18:45,795] [INFO] DFAST Taxonomy check result was written to GCA_934132995.1_ERR7746048_bin.75_genomic.fna/tc_result.tsv
[2023-06-05 01:18:45,796] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:18:45,796] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:18:45,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5493a14a-d764-4153-aec2-8fba42ff62ae/dqc_reference/checkm_data
[2023-06-05 01:18:45,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:18:45,818] [INFO] Task started: CheckM
[2023-06-05 01:18:45,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934132995.1_ERR7746048_bin.75_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934132995.1_ERR7746048_bin.75_genomic.fna/checkm_input GCA_934132995.1_ERR7746048_bin.75_genomic.fna/checkm_result
[2023-06-05 01:19:00,622] [INFO] Task succeeded: CheckM
[2023-06-05 01:19:00,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:19:00,641] [INFO] ===== Completeness check finished =====
[2023-06-05 01:19:00,641] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:19:00,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934132995.1_ERR7746048_bin.75_genomic.fna/markers.fasta)
[2023-06-05 01:19:00,642] [INFO] Task started: Blastn
[2023-06-05 01:19:00,642] [INFO] Running command: blastn -query GCA_934132995.1_ERR7746048_bin.75_genomic.fna/markers.fasta -db /var/lib/cwl/stg5493a14a-d764-4153-aec2-8fba42ff62ae/dqc_reference/reference_markers_gtdb.fasta -out GCA_934132995.1_ERR7746048_bin.75_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:19:01,518] [INFO] Task succeeded: Blastn
[2023-06-05 01:19:01,523] [INFO] Selected 20 target genomes.
[2023-06-05 01:19:01,523] [INFO] Target genome list was writen to GCA_934132995.1_ERR7746048_bin.75_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:19:01,525] [INFO] Task started: fastANI
[2023-06-05 01:19:01,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg07ffa22e-44bb-4d4e-94c2-88ae2388fd94/GCA_934132995.1_ERR7746048_bin.75_genomic.fna.gz --refList GCA_934132995.1_ERR7746048_bin.75_genomic.fna/target_genomes_gtdb.txt --output GCA_934132995.1_ERR7746048_bin.75_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:19:06,449] [INFO] Task succeeded: fastANI
[2023-06-05 01:19:06,465] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:19:06,465] [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_900769695.1	s__UMGS995 sp900769695	97.2135	317	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS995	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900547465.1	s__UMGS995 sp900547465	79.8702	187	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS995	95.0	98.53	97.90	0.89	0.89	3	-
GCA_902784095.1	s__UMGS995 sp902784095	78.9286	180	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432835.1	s__CAG-417 sp000432835	78.7657	83	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-417	95.0	98.45	98.23	0.92	0.90	4	-
GCA_905216155.1	s__Faecimonas sp905216155	78.3337	122	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586865.1	s__UMGS995 sp910586865	78.1927	127	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059435.1	s__Faecimonas sp015059435	78.1259	112	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622175.1	s__CAG-877 sp017622175	78.1016	99	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801525.1	s__RUG14670 sp902801525	77.9592	116	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG14670	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017416535.1	s__CAG-877 sp017416535	77.7483	101	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017519965.1	s__RUG14891 sp017519965	77.6428	87	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG14891	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902791625.1	s__CAG-417 sp902791625	77.6112	104	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017525855.1	s__CAG-417 sp017525855	77.4878	90	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712565.1	s__Faecimonas gallistercoris	77.3141	85	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	99.98	99.98	0.85	0.85	2	-
GCA_017510225.1	s__Faecimonas sp017510225	77.2896	91	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541885.1	s__UBA3789 sp017541885	77.2488	91	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002369415.1	s__UBA3789 sp002369415	77.1086	98	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715925.1	s__Onthousia faecipullorum	77.0298	75	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	99.48	99.48	0.89	0.89	2	-
GCA_002477275.1	s__CAG-417 sp002477275	76.6548	99	432	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-417	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:19:06,467] [INFO] GTDB search result was written to GCA_934132995.1_ERR7746048_bin.75_genomic.fna/result_gtdb.tsv
[2023-06-05 01:19:06,468] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:19:06,471] [INFO] DFAST_QC result json was written to GCA_934132995.1_ERR7746048_bin.75_genomic.fna/dqc_result.json
[2023-06-05 01:19:06,472] [INFO] DFAST_QC completed!
[2023-06-05 01:19:06,472] [INFO] Total running time: 0h0m37s