[2023-06-29 12:21:34,696] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:21:34,699] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:21:34,699] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bd6f09b-4028-4732-972a-8dc60a25c613/dqc_reference
[2023-06-29 12:21:35,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:21:35,967] [INFO] Task started: Prodigal
[2023-06-29 12:21:35,968] [INFO] Running command: gunzip -c /var/lib/cwl/stge05a3676-3432-41cf-8c2c-4da44173a816/GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:21:54,570] [INFO] Task succeeded: Prodigal
[2023-06-29 12:21:54,571] [INFO] Task started: HMMsearch
[2023-06-29 12:21:54,571] [INFO] Running command: hmmsearch --tblout GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bd6f09b-4028-4732-972a-8dc60a25c613/dqc_reference/reference_markers.hmm GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:21:54,828] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:21:54,829] [INFO] Found 6/6 markers.
[2023-06-29 12:21:54,859] [INFO] Query marker FASTA was written to GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 12:21:54,860] [INFO] Task started: Blastn
[2023-06-29 12:21:54,860] [INFO] Running command: blastn -query GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bd6f09b-4028-4732-972a-8dc60a25c613/dqc_reference/reference_markers.fasta -out GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:21:55,443] [INFO] Task succeeded: Blastn
[2023-06-29 12:21:55,447] [INFO] Selected 27 target genomes.
[2023-06-29 12:21:55,447] [INFO] Target genome list was writen to GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 12:21:55,451] [INFO] Task started: fastANI
[2023-06-29 12:21:55,451] [INFO] Running command: fastANI --query /var/lib/cwl/stge05a3676-3432-41cf-8c2c-4da44173a816/GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:22:12,915] [INFO] Task succeeded: fastANI
[2023-06-29 12:22:12,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bd6f09b-4028-4732-972a-8dc60a25c613/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:22:12,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bd6f09b-4028-4732-972a-8dc60a25c613/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:22:12,919] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:22:12,919] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 12:22:12,919] [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 12:22:12,922] [INFO] DFAST Taxonomy check result was written to GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 12:22:12,922] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:22:12,923] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:22:12,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bd6f09b-4028-4732-972a-8dc60a25c613/dqc_reference/checkm_data
[2023-06-29 12:22:12,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:22:12,958] [INFO] Task started: CheckM
[2023-06-29 12:22:12,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 12:23:07,390] [INFO] Task succeeded: CheckM
[2023-06-29 12:23:07,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.84%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:23:07,413] [INFO] ===== Completeness check finished =====
[2023-06-29 12:23:07,414] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:23:07,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 12:23:07,415] [INFO] Task started: Blastn
[2023-06-29 12:23:07,415] [INFO] Running command: blastn -query GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bd6f09b-4028-4732-972a-8dc60a25c613/dqc_reference/reference_markers_gtdb.fasta -out GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:23:08,200] [INFO] Task succeeded: Blastn
[2023-06-29 12:23:08,205] [INFO] Selected 21 target genomes.
[2023-06-29 12:23:08,205] [INFO] Target genome list was writen to GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:23:08,215] [INFO] Task started: fastANI
[2023-06-29 12:23:08,216] [INFO] Running command: fastANI --query /var/lib/cwl/stge05a3676-3432-41cf-8c2c-4da44173a816/GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:23:18,513] [INFO] Task succeeded: fastANI
[2023-06-29 12:23:18,525] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:23:18,525] [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_017649855.1	s__F23-D06 sp017649855	80.0313	360	912	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017544105.1	s__F23-D06 sp017544105	79.6608	285	912	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017650305.1	s__F23-D06 sp017650305	79.6057	270	912	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017549765.1	s__F23-D06 sp017549765	79.2847	319	912	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017615595.1	s__F23-D06 sp017615595	78.9456	265	912	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315705.1	s__F23-D06 sp900315705	78.4032	177	912	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	96.57	95.67	0.83	0.75	8	-
GCA_016285145.1	s__F23-D06 sp016285145	78.3992	152	912	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017554325.1	s__F23-D06 sp017554325	78.0038	140	912	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551725.1	s__F23-D06 sp017551725	77.9407	134	912	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002311645.1	s__F23-D06 sp002311645	77.2675	111	912	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	99.56	99.21	0.92	0.91	3	-
GCA_017535665.1	s__UBA1756 sp017535665	76.4418	73	912	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__UBA1756	95.0	96.47	96.07	0.85	0.80	3	-
--------------------------------------------------------------------------------
[2023-06-29 12:23:18,527] [INFO] GTDB search result was written to GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 12:23:18,528] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:23:18,530] [INFO] DFAST_QC result json was written to GCA_937901455.1_ERR1278073_bin.58_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 12:23:18,530] [INFO] DFAST_QC completed!
[2023-06-29 12:23:18,530] [INFO] Total running time: 0h1m44s