[2023-06-30 16:28:58,787] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:28:58,792] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:28:58,792] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2c07251-4dbe-4e14-a70a-fdcc74f2fdb3/dqc_reference
[2023-06-30 16:29:00,197] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:29:00,199] [INFO] Task started: Prodigal
[2023-06-30 16:29:00,200] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3ec73e4-d5c4-4c33-a38d-4475fc9798f3/GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna.gz | prodigal -d GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/cds.fna -a GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:29:08,495] [INFO] Task succeeded: Prodigal
[2023-06-30 16:29:08,496] [INFO] Task started: HMMsearch
[2023-06-30 16:29:08,496] [INFO] Running command: hmmsearch --tblout GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2c07251-4dbe-4e14-a70a-fdcc74f2fdb3/dqc_reference/reference_markers.hmm GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:29:08,782] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:29:08,783] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb3ec73e4-d5c4-4c33-a38d-4475fc9798f3/GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna.gz]
[2023-06-30 16:29:08,816] [INFO] Query marker FASTA was written to GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/markers.fasta
[2023-06-30 16:29:08,817] [INFO] Task started: Blastn
[2023-06-30 16:29:08,817] [INFO] Running command: blastn -query GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2c07251-4dbe-4e14-a70a-fdcc74f2fdb3/dqc_reference/reference_markers.fasta -out GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:29:09,530] [INFO] Task succeeded: Blastn
[2023-06-30 16:29:09,534] [INFO] Selected 25 target genomes.
[2023-06-30 16:29:09,535] [INFO] Target genome list was writen to GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/target_genomes.txt
[2023-06-30 16:29:09,537] [INFO] Task started: fastANI
[2023-06-30 16:29:09,537] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3ec73e4-d5c4-4c33-a38d-4475fc9798f3/GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna.gz --refList GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/target_genomes.txt --output GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:29:28,997] [INFO] Task succeeded: fastANI
[2023-06-30 16:29:28,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2c07251-4dbe-4e14-a70a-fdcc74f2fdb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:29:28,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2c07251-4dbe-4e14-a70a-fdcc74f2fdb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:29:29,013] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:29:29,013] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 16:29:29,013] [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
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	75.1319	79	633	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	75.0605	107	633	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	75.0463	77	633	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	75.038	97	633	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	74.8907	52	633	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	74.8705	63	633	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	74.8485	65	633	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	74.8427	66	633	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	74.8411	66	633	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.825	83	633	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.8113	158	633	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.8098	161	633	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	74.8067	69	633	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	74.7977	71	633	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	74.733	122	633	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 16:29:29,036] [INFO] DFAST Taxonomy check result was written to GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/tc_result.tsv
[2023-06-30 16:29:29,036] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:29:29,036] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:29:29,037] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2c07251-4dbe-4e14-a70a-fdcc74f2fdb3/dqc_reference/checkm_data
[2023-06-30 16:29:29,038] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:29:29,073] [INFO] Task started: CheckM
[2023-06-30 16:29:29,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/checkm_input GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/checkm_result
[2023-06-30 16:29:57,291] [INFO] Task succeeded: CheckM
[2023-06-30 16:29:57,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 16:29:57,313] [INFO] ===== Completeness check finished =====
[2023-06-30 16:29:57,314] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:29:57,314] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/markers.fasta)
[2023-06-30 16:29:57,315] [INFO] Task started: Blastn
[2023-06-30 16:29:57,315] [INFO] Running command: blastn -query GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2c07251-4dbe-4e14-a70a-fdcc74f2fdb3/dqc_reference/reference_markers_gtdb.fasta -out GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:29:58,315] [INFO] Task succeeded: Blastn
[2023-06-30 16:29:58,318] [INFO] Selected 6 target genomes.
[2023-06-30 16:29:58,319] [INFO] Target genome list was writen to GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:29:58,323] [INFO] Task started: fastANI
[2023-06-30 16:29:58,323] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3ec73e4-d5c4-4c33-a38d-4475fc9798f3/GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna.gz --refList GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/target_genomes_gtdb.txt --output GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:30:03,154] [INFO] Task succeeded: fastANI
[2023-06-30 16:30:03,166] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 16:30:03,166] [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_903859215.1	s__CAINDZ01 sp903859215	99.3568	593	633	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	99.58	99.58	0.89	0.89	2	conclusive
GCA_903912525.1	s__CAINDZ01 sp903912525	89.1841	567	633	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847545.1	s__CAINDZ01 sp903847545	86.4069	411	633	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	98.70	98.54	0.79	0.77	4	-
GCA_016703265.1	s__CAINDZ01 sp016703265	82.8279	447	633	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	96.41	95.95	0.89	0.87	7	-
GCA_016712675.1	s__CAINDZ01 sp016712675	82.2759	428	633	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873405.1	s__CAINDZ01 sp016873405	81.4914	235	633	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 16:30:03,168] [INFO] GTDB search result was written to GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/result_gtdb.tsv
[2023-06-30 16:30:03,168] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:30:03,172] [INFO] DFAST_QC result json was written to GCA_903916975.1_freshwater_MAG_---_LJ-3-65m_bin-0064_genomic.fna/dqc_result.json
[2023-06-30 16:30:03,172] [INFO] DFAST_QC completed!
[2023-06-30 16:30:03,173] [INFO] Total running time: 0h1m4s