[2023-06-29 23:36:39,201] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:36:39,203] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:36:39,203] [INFO] DQC Reference Directory: /var/lib/cwl/stgc635f9e7-9b17-4311-bf6d-8ebd2771711f/dqc_reference
[2023-06-29 23:36:40,397] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:36:40,398] [INFO] Task started: Prodigal
[2023-06-29 23:36:40,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg15f53a48-1075-431b-a4f5-edcd8fb5cb7d/GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna.gz | prodigal -d GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/cds.fna -a GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:37:12,065] [INFO] Task succeeded: Prodigal
[2023-06-29 23:37:12,066] [INFO] Task started: HMMsearch
[2023-06-29 23:37:12,066] [INFO] Running command: hmmsearch --tblout GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc635f9e7-9b17-4311-bf6d-8ebd2771711f/dqc_reference/reference_markers.hmm GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:37:12,378] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:37:12,380] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg15f53a48-1075-431b-a4f5-edcd8fb5cb7d/GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna.gz]
[2023-06-29 23:37:12,429] [INFO] Query marker FASTA was written to GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/markers.fasta
[2023-06-29 23:37:12,430] [INFO] Task started: Blastn
[2023-06-29 23:37:12,430] [INFO] Running command: blastn -query GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/markers.fasta -db /var/lib/cwl/stgc635f9e7-9b17-4311-bf6d-8ebd2771711f/dqc_reference/reference_markers.fasta -out GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:37:13,019] [INFO] Task succeeded: Blastn
[2023-06-29 23:37:13,023] [INFO] Selected 12 target genomes.
[2023-06-29 23:37:13,024] [INFO] Target genome list was writen to GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/target_genomes.txt
[2023-06-29 23:37:13,027] [INFO] Task started: fastANI
[2023-06-29 23:37:13,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg15f53a48-1075-431b-a4f5-edcd8fb5cb7d/GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna.gz --refList GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/target_genomes.txt --output GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:37:20,680] [INFO] Task succeeded: fastANI
[2023-06-29 23:37:20,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc635f9e7-9b17-4311-bf6d-8ebd2771711f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:37:20,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc635f9e7-9b17-4311-bf6d-8ebd2771711f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:37:20,693] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:37:20,693] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:37:20,694] [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	77.0302	132	1402	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	76.9926	180	1402	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.4018	91	1402	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	76.3638	131	1402	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	76.2903	72	1402	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	76.1779	84	1402	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	74.6577	73	1402	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:37:20,696] [INFO] DFAST Taxonomy check result was written to GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/tc_result.tsv
[2023-06-29 23:37:20,697] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:37:20,697] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:37:20,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc635f9e7-9b17-4311-bf6d-8ebd2771711f/dqc_reference/checkm_data
[2023-06-29 23:37:20,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:37:20,757] [INFO] Task started: CheckM
[2023-06-29 23:37:20,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/checkm_input GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/checkm_result
[2023-06-29 23:38:43,419] [INFO] Task succeeded: CheckM
[2023-06-29 23:38:43,421] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.02%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:38:43,448] [INFO] ===== Completeness check finished =====
[2023-06-29 23:38:43,448] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:38:43,448] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/markers.fasta)
[2023-06-29 23:38:43,449] [INFO] Task started: Blastn
[2023-06-29 23:38:43,449] [INFO] Running command: blastn -query GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/markers.fasta -db /var/lib/cwl/stgc635f9e7-9b17-4311-bf6d-8ebd2771711f/dqc_reference/reference_markers_gtdb.fasta -out GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:38:44,211] [INFO] Task succeeded: Blastn
[2023-06-29 23:38:44,216] [INFO] Selected 16 target genomes.
[2023-06-29 23:38:44,216] [INFO] Target genome list was writen to GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:38:44,223] [INFO] Task started: fastANI
[2023-06-29 23:38:44,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg15f53a48-1075-431b-a4f5-edcd8fb5cb7d/GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna.gz --refList GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/target_genomes_gtdb.txt --output GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:38:56,456] [INFO] Task succeeded: fastANI
[2023-06-29 23:38:56,474] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 23:38:56,474] [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_005799525.1	s__CAITWF01 sp005799525	91.4579	861	1402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903948415.1	s__CAITWF01 sp903948415	82.7673	751	1402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304445.1	s__Tous-C4FEB sp002304445	79.3667	313	1402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	98.22	97.15	0.85	0.81	4	-
GCA_009695305.1	s__CAITWF01 sp009695305	79.1074	397	1402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737275.1	s__Tous-C4FEB sp002737275	78.9935	212	1402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938935.1	s__Tous-C4FEB sp903938935	78.4666	227	1402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	98.58	98.56	0.78	0.76	6	-
GCA_903919985.1	s__Tous-C4FEB sp903919985	78.2533	128	1402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235555.1	s__ER46 sp016235555	77.9031	471	1402	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	77.7257	229	1402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903859715.1	s__Opi-474 sp903859715	77.4902	172	1402	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_903820035.1	s__ER46 sp903820035	77.4357	319	1402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	99.61	99.58	0.90	0.89	3	-
GCA_903840415.1	s__CAITWF01 sp903840415	77.3051	231	1402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	99.98	99.98	0.98	0.97	3	-
GCA_903877135.1	s__Opitutus sp903877135	77.1881	199	1402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	99.97	99.95	0.97	0.97	4	-
GCA_903881475.1	s__Opi-474 sp903881475	77.0538	170	1402	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_007559335.1	s__Rariglobus hedericola	77.0486	131	1402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861185.1	s__ER46 sp903861185	75.8284	173	1402	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:38:56,476] [INFO] GTDB search result was written to GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/result_gtdb.tsv
[2023-06-29 23:38:56,476] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:38:56,480] [INFO] DFAST_QC result json was written to GCA_903960155.1_freshwater_MAG_---_Loc090519-1m_bin-2180_genomic.fna/dqc_result.json
[2023-06-29 23:38:56,480] [INFO] DFAST_QC completed!
[2023-06-29 23:38:56,481] [INFO] Total running time: 0h2m17s