[2023-06-30 04:21:20,582] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:21:20,586] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:21:20,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg372c4bad-9ddd-464e-af07-0fbeddf993ba/dqc_reference
[2023-06-30 04:21:22,852] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:21:22,853] [INFO] Task started: Prodigal
[2023-06-30 04:21:22,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e79adf3-8d0d-4c98-8d3e-536ef3bef88c/GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna.gz | prodigal -d GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/cds.fna -a GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:21:43,025] [INFO] Task succeeded: Prodigal
[2023-06-30 04:21:43,026] [INFO] Task started: HMMsearch
[2023-06-30 04:21:43,026] [INFO] Running command: hmmsearch --tblout GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg372c4bad-9ddd-464e-af07-0fbeddf993ba/dqc_reference/reference_markers.hmm GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:21:43,265] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:21:43,267] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9e79adf3-8d0d-4c98-8d3e-536ef3bef88c/GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna.gz]
[2023-06-30 04:21:43,303] [INFO] Query marker FASTA was written to GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/markers.fasta
[2023-06-30 04:21:43,303] [INFO] Task started: Blastn
[2023-06-30 04:21:43,304] [INFO] Running command: blastn -query GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/markers.fasta -db /var/lib/cwl/stg372c4bad-9ddd-464e-af07-0fbeddf993ba/dqc_reference/reference_markers.fasta -out GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:21:43,966] [INFO] Task succeeded: Blastn
[2023-06-30 04:21:43,972] [INFO] Selected 14 target genomes.
[2023-06-30 04:21:43,972] [INFO] Target genome list was writen to GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/target_genomes.txt
[2023-06-30 04:21:43,975] [INFO] Task started: fastANI
[2023-06-30 04:21:43,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e79adf3-8d0d-4c98-8d3e-536ef3bef88c/GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna.gz --refList GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/target_genomes.txt --output GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:21:52,111] [INFO] Task succeeded: fastANI
[2023-06-30 04:21:52,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg372c4bad-9ddd-464e-af07-0fbeddf993ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:21:52,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg372c4bad-9ddd-464e-af07-0fbeddf993ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:21:52,121] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:21:52,121] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 04:21:52,121] [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
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	77.9389	173	919	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	77.654	281	919	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	77.5139	199	919	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	77.1303	132	919	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	76.8118	132	919	95	below_threshold
Cephaloticoccus capnophilus	strain=CV41	GCA_001580045.1	1548208	1548208	type	True	76.5647	88	919	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.5607	133	919	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 04:21:52,124] [INFO] DFAST Taxonomy check result was written to GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/tc_result.tsv
[2023-06-30 04:21:52,124] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:21:52,124] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:21:52,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg372c4bad-9ddd-464e-af07-0fbeddf993ba/dqc_reference/checkm_data
[2023-06-30 04:21:52,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:21:52,161] [INFO] Task started: CheckM
[2023-06-30 04:21:52,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/checkm_input GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/checkm_result
[2023-06-30 04:22:46,717] [INFO] Task succeeded: CheckM
[2023-06-30 04:22:46,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.24%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 04:22:46,744] [INFO] ===== Completeness check finished =====
[2023-06-30 04:22:46,744] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:22:46,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/markers.fasta)
[2023-06-30 04:22:46,745] [INFO] Task started: Blastn
[2023-06-30 04:22:46,745] [INFO] Running command: blastn -query GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/markers.fasta -db /var/lib/cwl/stg372c4bad-9ddd-464e-af07-0fbeddf993ba/dqc_reference/reference_markers_gtdb.fasta -out GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:22:47,774] [INFO] Task succeeded: Blastn
[2023-06-30 04:22:47,779] [INFO] Selected 11 target genomes.
[2023-06-30 04:22:47,779] [INFO] Target genome list was writen to GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:22:47,782] [INFO] Task started: fastANI
[2023-06-30 04:22:47,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e79adf3-8d0d-4c98-8d3e-536ef3bef88c/GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna.gz --refList GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/target_genomes_gtdb.txt --output GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:22:55,204] [INFO] Task succeeded: fastANI
[2023-06-30 04:22:55,225] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:22:55,226] [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_903862955.1	s__Opi-474 sp903862955	99.9461	891	919	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.96	99.95	0.97	0.97	5	conclusive
GCA_903855985.1	s__Opi-474 sp903855985	83.2442	570	919	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.84	99.84	0.94	0.94	2	-
GCA_903839035.1	s__Opi-474 sp903839035	82.856	610	919	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.67	99.48	0.93	0.89	8	-
GCA_003402695.1	s__Opi-474 sp003402695	82.5624	480	919	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903872505.1	s__Opi-474 sp903872505	82.3469	613	919	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.99	99.98	0.99	0.99	3	-
GCA_903825285.1	s__Opi-474 sp903825285	81.4235	577	919	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.78	99.55	0.96	0.94	12	-
GCA_903830425.1	s__Opi-474 sp903830425	80.5829	468	919	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.49	99.28	0.91	0.87	25	-
GCA_903859715.1	s__Opi-474 sp903859715	80.5269	473	919	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.98	99.96	0.98	0.96	7	-
GCA_903881475.1	s__Opi-474 sp903881475	80.5237	501	919	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.50	98.31	0.92	0.83	9	-
GCF_900104925.1	s__Lacunisphaera sp900104925	78.82	289	919	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016190985.1	s__Lacunisphaera sp016190985	78.5419	263	919	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:22:55,228] [INFO] GTDB search result was written to GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/result_gtdb.tsv
[2023-06-30 04:22:55,229] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:22:55,233] [INFO] DFAST_QC result json was written to GCA_903913455.1_freshwater_MAG_---_AM5_bin-1211_genomic.fna/dqc_result.json
[2023-06-30 04:22:55,233] [INFO] DFAST_QC completed!
[2023-06-30 04:22:55,233] [INFO] Total running time: 0h1m35s