[2023-06-30 00:55:13,774] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:55:13,776] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:55:13,776] [INFO] DQC Reference Directory: /var/lib/cwl/stg24ddb241-8b1f-4225-b0e6-ea05df14394e/dqc_reference
[2023-06-30 00:55:15,075] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:55:15,076] [INFO] Task started: Prodigal
[2023-06-30 00:55:15,076] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe79b207-a684-4808-a90a-ad2a34dd3738/GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna.gz | prodigal -d GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/cds.fna -a GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:55:35,707] [INFO] Task succeeded: Prodigal
[2023-06-30 00:55:35,708] [INFO] Task started: HMMsearch
[2023-06-30 00:55:35,708] [INFO] Running command: hmmsearch --tblout GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24ddb241-8b1f-4225-b0e6-ea05df14394e/dqc_reference/reference_markers.hmm GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:55:35,961] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:55:35,962] [INFO] Found 6/6 markers.
[2023-06-30 00:55:35,996] [INFO] Query marker FASTA was written to GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/markers.fasta
[2023-06-30 00:55:35,996] [INFO] Task started: Blastn
[2023-06-30 00:55:35,996] [INFO] Running command: blastn -query GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/markers.fasta -db /var/lib/cwl/stg24ddb241-8b1f-4225-b0e6-ea05df14394e/dqc_reference/reference_markers.fasta -out GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:55:36,608] [INFO] Task succeeded: Blastn
[2023-06-30 00:55:36,613] [INFO] Selected 12 target genomes.
[2023-06-30 00:55:36,614] [INFO] Target genome list was writen to GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/target_genomes.txt
[2023-06-30 00:55:36,616] [INFO] Task started: fastANI
[2023-06-30 00:55:36,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe79b207-a684-4808-a90a-ad2a34dd3738/GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna.gz --refList GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/target_genomes.txt --output GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:55:43,216] [INFO] Task succeeded: fastANI
[2023-06-30 00:55:43,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24ddb241-8b1f-4225-b0e6-ea05df14394e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:55:43,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24ddb241-8b1f-4225-b0e6-ea05df14394e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:55:43,228] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:55:43,228] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:55:43,228] [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
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	77.5264	214	990	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	77.2531	121	990	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	77.0225	85	990	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	76.8818	149	990	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.4708	86	990	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	76.368	98	990	95	below_threshold
Cephaloticoccus capnophilus	strain=CV41	GCA_001580045.1	1548208	1548208	type	True	75.8221	55	990	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:55:43,230] [INFO] DFAST Taxonomy check result was written to GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/tc_result.tsv
[2023-06-30 00:55:43,231] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:55:43,232] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:55:43,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24ddb241-8b1f-4225-b0e6-ea05df14394e/dqc_reference/checkm_data
[2023-06-30 00:55:43,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:55:43,275] [INFO] Task started: CheckM
[2023-06-30 00:55:43,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/checkm_input GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/checkm_result
[2023-06-30 00:56:40,305] [INFO] Task succeeded: CheckM
[2023-06-30 00:56:40,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:56:40,327] [INFO] ===== Completeness check finished =====
[2023-06-30 00:56:40,328] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:56:40,328] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/markers.fasta)
[2023-06-30 00:56:40,329] [INFO] Task started: Blastn
[2023-06-30 00:56:40,329] [INFO] Running command: blastn -query GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/markers.fasta -db /var/lib/cwl/stg24ddb241-8b1f-4225-b0e6-ea05df14394e/dqc_reference/reference_markers_gtdb.fasta -out GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:56:41,195] [INFO] Task succeeded: Blastn
[2023-06-30 00:56:41,202] [INFO] Selected 20 target genomes.
[2023-06-30 00:56:41,202] [INFO] Target genome list was writen to GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:56:41,210] [INFO] Task started: fastANI
[2023-06-30 00:56:41,210] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe79b207-a684-4808-a90a-ad2a34dd3738/GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna.gz --refList GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/target_genomes_gtdb.txt --output GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:56:56,558] [INFO] Task succeeded: fastANI
[2023-06-30 00:56:56,576] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 00:56:56,577] [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_903848965.1	s__ER46 sp903848965	100.0	968	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016793535.1	s__ER46 sp016793535	78.274	300	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002288455.1	s__ER46 sp002288455	78.2293	274	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018239845.1	s__Opitutus sp018239845	78.1898	248	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715765.1	s__UBA2377 sp016715765	78.0645	199	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794785.1	s__ER46 sp016794785	77.9373	333	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009695065.1	s__ER46 sp009695065	77.9353	218	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	96.54	96.54	0.63	0.63	2	-
GCA_903872505.1	s__Opi-474 sp903872505	77.8786	243	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.99	99.98	0.99	0.99	3	-
GCF_003054705.1	s__ER46 sp003054705	77.8419	272	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903840415.1	s__CAITWF01 sp903840415	77.8347	230	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	99.98	99.98	0.98	0.97	3	-
GCA_903925425.1	s__CAIYFD01 sp903925425	77.7988	176	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIYFD01	95.0	98.64	98.42	0.84	0.82	3	-
GCA_016235555.1	s__ER46 sp016235555	77.7929	317	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209255.1	s__ER46 sp016209255	77.7546	250	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881475.1	s__Opi-474 sp903881475	77.6167	214	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.50	98.31	0.92	0.83	9	-
GCA_903896015.1	s__CAITWF01 sp903896015	77.4913	251	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	99.72	99.39	0.95	0.93	8	-
GCA_016871775.1	s__ER46 sp016871775	77.24	162	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871595.1	s__ER46 sp016871595	77.2305	167	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009695095.1	s__Lacunisphaera sp009695095	77.149	104	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916755.1	s__Palsa-1447 sp903916755	77.0227	139	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Palsa-1447	95.0	99.68	99.68	0.97	0.97	2	-
GCA_013822585.1	s__Didemnitutus sp013822585	76.343	110	990	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:56:56,579] [INFO] GTDB search result was written to GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/result_gtdb.tsv
[2023-06-30 00:56:56,579] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:56:56,583] [INFO] DFAST_QC result json was written to GCA_903848965.1_freshwater_MAG_---_UppL3_bin-435_genomic.fna/dqc_result.json
[2023-06-30 00:56:56,583] [INFO] DFAST_QC completed!
[2023-06-30 00:56:56,583] [INFO] Total running time: 0h1m43s