[2023-07-01 03:04:22,799] [INFO] DFAST_QC pipeline started.
[2023-07-01 03:04:22,801] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 03:04:22,802] [INFO] DQC Reference Directory: /var/lib/cwl/stg95c9d77e-8c85-4abe-9c10-b9adfe2dd254/dqc_reference
[2023-07-01 03:04:24,250] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 03:04:24,253] [INFO] Task started: Prodigal
[2023-07-01 03:04:24,253] [INFO] Running command: gunzip -c /var/lib/cwl/stg83b728df-325d-4360-b962-6e60320c60fc/GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna.gz | prodigal -d GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/cds.fna -a GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 03:04:43,178] [INFO] Task succeeded: Prodigal
[2023-07-01 03:04:43,179] [INFO] Task started: HMMsearch
[2023-07-01 03:04:43,179] [INFO] Running command: hmmsearch --tblout GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95c9d77e-8c85-4abe-9c10-b9adfe2dd254/dqc_reference/reference_markers.hmm GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/protein.faa > /dev/null
[2023-07-01 03:04:43,443] [INFO] Task succeeded: HMMsearch
[2023-07-01 03:04:43,444] [INFO] Found 6/6 markers.
[2023-07-01 03:04:43,481] [INFO] Query marker FASTA was written to GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/markers.fasta
[2023-07-01 03:04:43,481] [INFO] Task started: Blastn
[2023-07-01 03:04:43,481] [INFO] Running command: blastn -query GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/markers.fasta -db /var/lib/cwl/stg95c9d77e-8c85-4abe-9c10-b9adfe2dd254/dqc_reference/reference_markers.fasta -out GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:04:44,268] [INFO] Task succeeded: Blastn
[2023-07-01 03:04:44,292] [INFO] Selected 15 target genomes.
[2023-07-01 03:04:44,293] [INFO] Target genome list was writen to GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/target_genomes.txt
[2023-07-01 03:04:44,293] [INFO] Task started: fastANI
[2023-07-01 03:04:44,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg83b728df-325d-4360-b962-6e60320c60fc/GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna.gz --refList GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/target_genomes.txt --output GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 03:04:56,162] [INFO] Task succeeded: fastANI
[2023-07-01 03:04:56,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95c9d77e-8c85-4abe-9c10-b9adfe2dd254/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 03:04:56,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95c9d77e-8c85-4abe-9c10-b9adfe2dd254/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 03:04:56,174] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 03:04:56,174] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 03:04:56,175] [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
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	78.1443	184	1048	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	78.054	362	1048	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	77.7823	209	1048	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	77.5282	274	1048	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	77.2508	189	1048	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	77.2123	176	1048	95	below_threshold
Ruficoccus amylovorans	strain=JCM31066	GCA_014230085.1	1804625	1804625	type	True	76.3682	96	1048	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.09	110	1048	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	74.9976	74	1048	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	74.964	71	1048	95	below_threshold
Deinococcus aquiradiocola	strain=JCM 14371	GCA_014646915.1	393059	393059	type	True	74.8557	68	1048	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	74.7845	59	1048	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	74.7817	77	1048	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	74.7475	88	1048	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 03:04:56,199] [INFO] DFAST Taxonomy check result was written to GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/tc_result.tsv
[2023-07-01 03:04:56,200] [INFO] ===== Taxonomy check completed =====
[2023-07-01 03:04:56,200] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 03:04:56,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95c9d77e-8c85-4abe-9c10-b9adfe2dd254/dqc_reference/checkm_data
[2023-07-01 03:04:56,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 03:04:56,237] [INFO] Task started: CheckM
[2023-07-01 03:04:56,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/checkm_input GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/checkm_result
[2023-07-01 03:05:47,341] [INFO] Task succeeded: CheckM
[2023-07-01 03:05:47,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 03:05:47,363] [INFO] ===== Completeness check finished =====
[2023-07-01 03:05:47,364] [INFO] ===== Start GTDB Search =====
[2023-07-01 03:05:47,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/markers.fasta)
[2023-07-01 03:05:47,365] [INFO] Task started: Blastn
[2023-07-01 03:05:47,365] [INFO] Running command: blastn -query GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/markers.fasta -db /var/lib/cwl/stg95c9d77e-8c85-4abe-9c10-b9adfe2dd254/dqc_reference/reference_markers_gtdb.fasta -out GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:05:48,653] [INFO] Task succeeded: Blastn
[2023-07-01 03:05:48,657] [INFO] Selected 12 target genomes.
[2023-07-01 03:05:48,657] [INFO] Target genome list was writen to GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 03:05:48,658] [INFO] Task started: fastANI
[2023-07-01 03:05:48,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg83b728df-325d-4360-b962-6e60320c60fc/GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna.gz --refList GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/target_genomes_gtdb.txt --output GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 03:05:57,421] [INFO] Task succeeded: fastANI
[2023-07-01 03:05:57,443] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 03:05:57,444] [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_903830425.1	s__Opi-474 sp903830425	99.7129	940	1048	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.49	99.28	0.91	0.87	25	conclusive
GCA_903825285.1	s__Opi-474 sp903825285	83.0142	725	1048	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_903872505.1	s__Opi-474 sp903872505	82.4807	673	1048	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_903881475.1	s__Opi-474 sp903881475	82.3894	588	1048	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_903859715.1	s__Opi-474 sp903859715	82.255	569	1048	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_903839035.1	s__Opi-474 sp903839035	81.8645	623	1048	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_903855985.1	s__Opi-474 sp903855985	81.7472	570	1048	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_003402695.1	s__Opi-474 sp003402695	81.6128	478	1048	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_903862955.1	s__Opi-474 sp903862955	80.8409	600	1048	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.96	99.95	0.97	0.97	5	-
GCA_016715765.1	s__UBA2377 sp016715765	80.0897	501	1048	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016190985.1	s__Lacunisphaera sp016190985	79.2932	344	1048	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898675.1	s__Lacunisphaera sp903898675	78.8744	340	1048	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	99.99	99.98	0.99	0.98	5	-
--------------------------------------------------------------------------------
[2023-07-01 03:05:57,446] [INFO] GTDB search result was written to GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/result_gtdb.tsv
[2023-07-01 03:05:57,446] [INFO] ===== GTDB Search completed =====
[2023-07-01 03:05:57,450] [INFO] DFAST_QC result json was written to GCA_903826175.1_freshwater_MAG_---_LJ-7-9m_bin-1276_genomic.fna/dqc_result.json
[2023-07-01 03:05:57,450] [INFO] DFAST_QC completed!
[2023-07-01 03:05:57,451] [INFO] Total running time: 0h1m35s