[2023-06-28 17:15:21,444] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:15:21,446] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:15:21,446] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d4068a0-5165-49e5-9cbb-41eb05420150/dqc_reference
[2023-06-28 17:15:22,888] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:15:22,889] [INFO] Task started: Prodigal
[2023-06-28 17:15:22,889] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1091f3e-8063-4e10-bffc-df420281086b/GCA_944322945.1_BRZ_AE_bin22_genomic.fna.gz | prodigal -d GCA_944322945.1_BRZ_AE_bin22_genomic.fna/cds.fna -a GCA_944322945.1_BRZ_AE_bin22_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:15:27,404] [INFO] Task succeeded: Prodigal
[2023-06-28 17:15:27,405] [INFO] Task started: HMMsearch
[2023-06-28 17:15:27,405] [INFO] Running command: hmmsearch --tblout GCA_944322945.1_BRZ_AE_bin22_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d4068a0-5165-49e5-9cbb-41eb05420150/dqc_reference/reference_markers.hmm GCA_944322945.1_BRZ_AE_bin22_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:15:27,658] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:15:27,660] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf1091f3e-8063-4e10-bffc-df420281086b/GCA_944322945.1_BRZ_AE_bin22_genomic.fna.gz]
[2023-06-28 17:15:27,687] [INFO] Query marker FASTA was written to GCA_944322945.1_BRZ_AE_bin22_genomic.fna/markers.fasta
[2023-06-28 17:15:27,688] [INFO] Task started: Blastn
[2023-06-28 17:15:27,688] [INFO] Running command: blastn -query GCA_944322945.1_BRZ_AE_bin22_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d4068a0-5165-49e5-9cbb-41eb05420150/dqc_reference/reference_markers.fasta -out GCA_944322945.1_BRZ_AE_bin22_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:15:28,280] [INFO] Task succeeded: Blastn
[2023-06-28 17:15:28,284] [INFO] Selected 15 target genomes.
[2023-06-28 17:15:28,284] [INFO] Target genome list was writen to GCA_944322945.1_BRZ_AE_bin22_genomic.fna/target_genomes.txt
[2023-06-28 17:15:28,288] [INFO] Task started: fastANI
[2023-06-28 17:15:28,289] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1091f3e-8063-4e10-bffc-df420281086b/GCA_944322945.1_BRZ_AE_bin22_genomic.fna.gz --refList GCA_944322945.1_BRZ_AE_bin22_genomic.fna/target_genomes.txt --output GCA_944322945.1_BRZ_AE_bin22_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:15:38,737] [INFO] Task succeeded: fastANI
[2023-06-28 17:15:38,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d4068a0-5165-49e5-9cbb-41eb05420150/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:15:38,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d4068a0-5165-49e5-9cbb-41eb05420150/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:15:38,739] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:15:38,739] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:15:38,739] [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
--------------------------------------------------------------------------------
[2023-06-28 17:15:38,741] [INFO] DFAST Taxonomy check result was written to GCA_944322945.1_BRZ_AE_bin22_genomic.fna/tc_result.tsv
[2023-06-28 17:15:38,741] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:15:38,741] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:15:38,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d4068a0-5165-49e5-9cbb-41eb05420150/dqc_reference/checkm_data
[2023-06-28 17:15:38,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:15:38,778] [INFO] Task started: CheckM
[2023-06-28 17:15:38,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944322945.1_BRZ_AE_bin22_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944322945.1_BRZ_AE_bin22_genomic.fna/checkm_input GCA_944322945.1_BRZ_AE_bin22_genomic.fna/checkm_result
[2023-06-28 17:16:00,892] [INFO] Task succeeded: CheckM
[2023-06-28 17:16:00,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:16:00,914] [INFO] ===== Completeness check finished =====
[2023-06-28 17:16:00,914] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:16:00,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944322945.1_BRZ_AE_bin22_genomic.fna/markers.fasta)
[2023-06-28 17:16:00,915] [INFO] Task started: Blastn
[2023-06-28 17:16:00,915] [INFO] Running command: blastn -query GCA_944322945.1_BRZ_AE_bin22_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d4068a0-5165-49e5-9cbb-41eb05420150/dqc_reference/reference_markers_gtdb.fasta -out GCA_944322945.1_BRZ_AE_bin22_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:16:01,830] [INFO] Task succeeded: Blastn
[2023-06-28 17:16:01,835] [INFO] Selected 21 target genomes.
[2023-06-28 17:16:01,835] [INFO] Target genome list was writen to GCA_944322945.1_BRZ_AE_bin22_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:16:01,845] [INFO] Task started: fastANI
[2023-06-28 17:16:01,845] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1091f3e-8063-4e10-bffc-df420281086b/GCA_944322945.1_BRZ_AE_bin22_genomic.fna.gz --refList GCA_944322945.1_BRZ_AE_bin22_genomic.fna/target_genomes_gtdb.txt --output GCA_944322945.1_BRZ_AE_bin22_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:16:09,824] [INFO] Task succeeded: fastANI
[2023-06-28 17:16:09,851] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:16:09,851] [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_000431315.1	s__Scatousia sp000431315	78.222	161	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	97.32	95.18	0.89	0.88	6	-
GCA_000437435.1	s__Stercorousia sp000437435	77.9138	136	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	97.52	97.52	0.91	0.91	3	-
GCA_905216055.1	s__Stercorousia sp905216055	77.8204	151	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438175.1	s__Stercorousia faecigallinarum	77.7771	150	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.53	97.95	0.88	0.85	4	-
GCA_000433095.1	s__Stercorousia sp000433095	77.7703	156	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	99.53	99.13	0.95	0.93	3	-
GCA_900548405.1	s__Stercorousia sp001917115	77.7441	146	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.35	95.50	0.91	0.85	8	-
GCA_905212085.1	s__Stercorousia sp905212085	77.6708	116	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554385.1	s__Scatousia sp900554385	77.6503	120	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	99.41	98.83	0.97	0.96	3	-
GCA_910588555.1	s__Stercorousia sp910588555	77.6278	153	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711035.1	s__Scatousia excrementigallinarum	77.6218	130	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	99.20	99.20	0.79	0.79	2	-
GCA_017694215.1	s__Scatousia excrementipullorum	77.5037	145	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551675.1	s__Stercorousia sp900551675	77.343	142	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	100.00	100.00	0.98	0.98	2	-
GCA_001765415.1	s__Stercorousia sp001765415	77.3298	113	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.74	98.70	0.94	0.93	5	-
GCA_900555175.1	s__Stercorousia sp900555175	77.318	99	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	100.00	100.00	0.94	0.94	2	-
GCA_900321895.1	s__Scatousia sp900321895	77.2312	85	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	98.96	98.54	0.97	0.93	4	-
GCA_900767135.1	s__Stercorousia sp900767135	77.0832	98	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801985.1	s__UBA2813 sp902801985	77.0529	79	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902791985.1	s__UBA2813 sp902791985	76.9939	73	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769355.1	s__Stercorousia sp900769355	76.979	99	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788345.1	s__UBA2813 sp902788345	76.9326	71	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792085.1	s__UBA2813 sp902792085	76.4098	91	690	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:16:09,853] [INFO] GTDB search result was written to GCA_944322945.1_BRZ_AE_bin22_genomic.fna/result_gtdb.tsv
[2023-06-28 17:16:09,854] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:16:09,858] [INFO] DFAST_QC result json was written to GCA_944322945.1_BRZ_AE_bin22_genomic.fna/dqc_result.json
[2023-06-28 17:16:09,858] [INFO] DFAST_QC completed!
[2023-06-28 17:16:09,859] [INFO] Total running time: 0h0m48s