[2023-06-08 02:08:03,003] [INFO] DFAST_QC pipeline started.
[2023-06-08 02:08:03,012] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 02:08:03,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg4801bf0a-f5a8-4e2e-bc1c-1c884ce05b7c/dqc_reference
[2023-06-08 02:08:05,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 02:08:05,161] [INFO] Task started: Prodigal
[2023-06-08 02:08:05,161] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d93f562-4b92-4c2e-b12d-2b4d8bc997b6/GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 02:08:07,218] [INFO] Task succeeded: Prodigal
[2023-06-08 02:08:07,218] [INFO] Task started: HMMsearch
[2023-06-08 02:08:07,219] [INFO] Running command: hmmsearch --tblout GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4801bf0a-f5a8-4e2e-bc1c-1c884ce05b7c/dqc_reference/reference_markers.hmm GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 02:08:07,436] [INFO] Task succeeded: HMMsearch
[2023-06-08 02:08:07,438] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5d93f562-4b92-4c2e-b12d-2b4d8bc997b6/GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 02:08:07,460] [INFO] Query marker FASTA was written to GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 02:08:07,460] [INFO] Task started: Blastn
[2023-06-08 02:08:07,460] [INFO] Running command: blastn -query GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4801bf0a-f5a8-4e2e-bc1c-1c884ce05b7c/dqc_reference/reference_markers.fasta -out GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:08:09,269] [INFO] Task succeeded: Blastn
[2023-06-08 02:08:09,272] [INFO] Selected 25 target genomes.
[2023-06-08 02:08:09,273] [INFO] Target genome list was writen to GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 02:08:09,276] [INFO] Task started: fastANI
[2023-06-08 02:08:09,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d93f562-4b92-4c2e-b12d-2b4d8bc997b6/GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 02:08:18,623] [INFO] Task succeeded: fastANI
[2023-06-08 02:08:18,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4801bf0a-f5a8-4e2e-bc1c-1c884ce05b7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 02:08:18,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4801bf0a-f5a8-4e2e-bc1c-1c884ce05b7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 02:08:18,627] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 02:08:18,627] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 02:08:18,627] [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
--------------------------------------------------------------------------------
[2023-06-08 02:08:18,629] [INFO] DFAST Taxonomy check result was written to GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 02:08:18,630] [INFO] ===== Taxonomy check completed =====
[2023-06-08 02:08:18,631] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 02:08:18,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4801bf0a-f5a8-4e2e-bc1c-1c884ce05b7c/dqc_reference/checkm_data
[2023-06-08 02:08:18,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 02:08:18,653] [INFO] Task started: CheckM
[2023-06-08 02:08:18,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 02:08:33,474] [INFO] Task succeeded: CheckM
[2023-06-08 02:08:33,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 02:08:33,494] [INFO] ===== Completeness check finished =====
[2023-06-08 02:08:33,494] [INFO] ===== Start GTDB Search =====
[2023-06-08 02:08:33,495] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 02:08:33,495] [INFO] Task started: Blastn
[2023-06-08 02:08:33,495] [INFO] Running command: blastn -query GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4801bf0a-f5a8-4e2e-bc1c-1c884ce05b7c/dqc_reference/reference_markers_gtdb.fasta -out GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:08:34,345] [INFO] Task succeeded: Blastn
[2023-06-08 02:08:34,349] [INFO] Selected 22 target genomes.
[2023-06-08 02:08:34,349] [INFO] Target genome list was writen to GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 02:08:34,353] [INFO] Task started: fastANI
[2023-06-08 02:08:34,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d93f562-4b92-4c2e-b12d-2b4d8bc997b6/GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 02:08:39,119] [INFO] Task succeeded: fastANI
[2023-06-08 02:08:39,136] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 02:08:39,136] [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_910586865.1	s__UMGS995 sp910586865	78.2067	81	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576925.1	s__UBA2730 sp910576925	78.1715	139	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA2730	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432835.1	s__CAG-417 sp000432835	77.6151	82	447	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_910583685.1	s__MGBC119817 sp910583685	77.5182	77	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__MGBC119817	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902791625.1	s__CAG-417 sp902791625	77.3568	73	447	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_015059435.1	s__Faecimonas sp015059435	77.3097	69	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780395.1	s__UBA3789 sp902780395	77.1522	57	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554315.1	s__Faecimonas sp900554315	77.0003	59	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	99.99	99.97	0.89	0.78	3	-
GCA_016293205.1	s__CAG-877 sp016293205	76.9597	66	447	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_900547465.1	s__UMGS995 sp900547465	76.836	57	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS995	95.0	98.53	97.90	0.89	0.89	3	-
GCA_900548695.1	s__Faecimonas sp900548695	76.6125	66	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017886705.1	s__Faecimonas sp017886705	76.5157	66	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552495.1	s__CAG-877 sp900552495	76.5023	62	447	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_900313345.1	s__UBA2730 sp900313345	76.3087	65	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA2730	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002477275.1	s__CAG-417 sp002477275	76.2617	70	447	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_902783435.1	s__UBA3789 sp902783435	75.9706	58	447	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 02:08:39,147] [INFO] GTDB search result was written to GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 02:08:39,148] [INFO] ===== GTDB Search completed =====
[2023-06-08 02:08:39,152] [INFO] DFAST_QC result json was written to GCA_947643225.1_SRR15730529_bin.44_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 02:08:39,152] [INFO] DFAST_QC completed!
[2023-06-08 02:08:39,152] [INFO] Total running time: 0h0m36s