[2023-06-13 00:23:49,242] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:23:49,245] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:23:49,245] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5a8e915-165a-4829-867d-c99603afc326/dqc_reference
[2023-06-13 00:23:50,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:23:50,536] [INFO] Task started: Prodigal
[2023-06-13 00:23:50,536] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8456ba7-db7c-4f36-8dbf-b83a9109ce53/GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:24:00,674] [INFO] Task succeeded: Prodigal
[2023-06-13 00:24:00,674] [INFO] Task started: HMMsearch
[2023-06-13 00:24:00,675] [INFO] Running command: hmmsearch --tblout GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5a8e915-165a-4829-867d-c99603afc326/dqc_reference/reference_markers.hmm GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:24:00,946] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:24:00,948] [INFO] Found 6/6 markers.
[2023-06-13 00:24:00,975] [INFO] Query marker FASTA was written to GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 00:24:00,975] [INFO] Task started: Blastn
[2023-06-13 00:24:00,975] [INFO] Running command: blastn -query GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5a8e915-165a-4829-867d-c99603afc326/dqc_reference/reference_markers.fasta -out GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:24:01,563] [INFO] Task succeeded: Blastn
[2023-06-13 00:24:01,567] [INFO] Selected 28 target genomes.
[2023-06-13 00:24:01,568] [INFO] Target genome list was writen to GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 00:24:01,572] [INFO] Task started: fastANI
[2023-06-13 00:24:01,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8456ba7-db7c-4f36-8dbf-b83a9109ce53/GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:24:17,214] [INFO] Task succeeded: fastANI
[2023-06-13 00:24:17,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5a8e915-165a-4829-867d-c99603afc326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:24:17,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5a8e915-165a-4829-867d-c99603afc326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:24:17,218] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:24:17,218] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 00:24:17,218] [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
--------------------------------------------------------------------------------
[2023-06-13 00:24:17,223] [INFO] DFAST Taxonomy check result was written to GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 00:24:17,224] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:24:17,224] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:24:17,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5a8e915-165a-4829-867d-c99603afc326/dqc_reference/checkm_data
[2023-06-13 00:24:17,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:24:17,255] [INFO] Task started: CheckM
[2023-06-13 00:24:17,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 00:24:50,354] [INFO] Task succeeded: CheckM
[2023-06-13 00:24:50,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.82%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:24:50,413] [INFO] ===== Completeness check finished =====
[2023-06-13 00:24:50,413] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:24:50,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 00:24:50,414] [INFO] Task started: Blastn
[2023-06-13 00:24:50,414] [INFO] Running command: blastn -query GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5a8e915-165a-4829-867d-c99603afc326/dqc_reference/reference_markers_gtdb.fasta -out GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:24:51,342] [INFO] Task succeeded: Blastn
[2023-06-13 00:24:51,349] [INFO] Selected 24 target genomes.
[2023-06-13 00:24:51,349] [INFO] Target genome list was writen to GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:24:51,376] [INFO] Task started: fastANI
[2023-06-13 00:24:51,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8456ba7-db7c-4f36-8dbf-b83a9109ce53/GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:25:00,250] [INFO] Task succeeded: fastANI
[2023-06-13 00:25:00,272] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 00:25:00,273] [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_017400135.1	s__Cryptobacteroides sp017400135	78.6625	197	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017477245.1	s__Cryptobacteroides sp017477245	78.3519	120	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.05	97.38	0.81	0.78	3	-
GCA_902782225.1	s__Cryptobacteroides sp902782225	78.1524	135	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.55	97.13	0.87	0.83	3	-
GCA_017471045.1	s__Cryptobacteroides sp017471045	78.1266	209	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017620335.1	s__Cryptobacteroides sp017620335	78.0468	141	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017438265.1	s__Cryptobacteroides sp017438265	77.8914	106	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.23	96.11	0.87	0.85	4	-
GCA_900319185.1	s__Cryptobacteroides sp900319185	77.8152	108	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.95	98.63	0.93	0.89	6	-
GCA_902780175.1	s__Cryptobacteroides sp902780175	77.7425	128	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	95.78	95.78	0.73	0.73	2	-
GCA_017455065.1	s__Cryptobacteroides sp017455065	77.5424	127	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017962165.1	s__Cryptobacteroides sp017962165	77.5406	73	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016288775.1	s__Cryptobacteroides sp016288775	77.5372	115	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001602865.1	s__Cryptobacteroides sp001602865	77.4968	81	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768665.1	s__Cryptobacteroides sp902768665	77.4428	110	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.70	96.60	0.87	0.83	3	-
GCA_017535125.1	s__Cryptobacteroides sp017535125	77.4336	99	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017453565.1	s__Cryptobacteroides sp017453565	77.39	92	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017695095.1	s__Cryptobacteroides avistercoris	77.3839	101	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.82	97.62	0.86	0.86	3	-
GCA_017553405.1	s__Cryptobacteroides sp017553405	77.3307	115	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551425.1	s__Cryptobacteroides sp017551425	77.2845	99	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017615615.1	s__Cryptobacteroides sp017615615	77.2761	104	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017960585.1	s__Cryptobacteroides sp017960585	76.9705	126	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233275.1	s__Cryptobacteroides sp905233275	76.847	86	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541925.1	s__Cryptobacteroides sp900541925	76.7538	81	613	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.89	97.86	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2023-06-13 00:25:00,275] [INFO] GTDB search result was written to GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 00:25:00,276] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:25:00,280] [INFO] DFAST_QC result json was written to GCA_947302175.1_SRR10912534_bin.30_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 00:25:00,280] [INFO] DFAST_QC completed!
[2023-06-13 00:25:00,280] [INFO] Total running time: 0h1m11s