[2023-06-30 04:32:52,365] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:32:52,367] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:32:52,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg8428b3e6-fcea-44a6-bd45-4efb65f15c34/dqc_reference
[2023-06-30 04:32:53,751] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:32:53,753] [INFO] Task started: Prodigal
[2023-06-30 04:32:53,753] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bb28444-bab8-4036-8339-97117ef086b2/GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna.gz | prodigal -d GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/cds.fna -a GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:33:00,536] [INFO] Task succeeded: Prodigal
[2023-06-30 04:33:00,536] [INFO] Task started: HMMsearch
[2023-06-30 04:33:00,536] [INFO] Running command: hmmsearch --tblout GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8428b3e6-fcea-44a6-bd45-4efb65f15c34/dqc_reference/reference_markers.hmm GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:33:00,804] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:33:00,805] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7bb28444-bab8-4036-8339-97117ef086b2/GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna.gz]
[2023-06-30 04:33:00,836] [INFO] Query marker FASTA was written to GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/markers.fasta
[2023-06-30 04:33:00,836] [INFO] Task started: Blastn
[2023-06-30 04:33:00,836] [INFO] Running command: blastn -query GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/markers.fasta -db /var/lib/cwl/stg8428b3e6-fcea-44a6-bd45-4efb65f15c34/dqc_reference/reference_markers.fasta -out GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:33:01,657] [INFO] Task succeeded: Blastn
[2023-06-30 04:33:01,661] [INFO] Selected 17 target genomes.
[2023-06-30 04:33:01,661] [INFO] Target genome list was writen to GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/target_genomes.txt
[2023-06-30 04:33:01,662] [INFO] Task started: fastANI
[2023-06-30 04:33:01,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bb28444-bab8-4036-8339-97117ef086b2/GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna.gz --refList GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/target_genomes.txt --output GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:33:13,954] [INFO] Task succeeded: fastANI
[2023-06-30 04:33:13,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8428b3e6-fcea-44a6-bd45-4efb65f15c34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:33:13,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8428b3e6-fcea-44a6-bd45-4efb65f15c34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:33:13,971] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:33:13,971] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 04:33:13,972] [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
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	77.1344	72	478	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	77.0351	63	478	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.9672	54	478	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	76.7967	57	478	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	76.76	71	478	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.6863	61	478	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	76.4737	67	478	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.442	70	478	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	76.3082	60	478	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.2462	79	478	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.2	85	478	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.0506	102	478	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	75.6058	56	478	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 04:33:13,975] [INFO] DFAST Taxonomy check result was written to GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/tc_result.tsv
[2023-06-30 04:33:13,976] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:33:13,976] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:33:13,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8428b3e6-fcea-44a6-bd45-4efb65f15c34/dqc_reference/checkm_data
[2023-06-30 04:33:13,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:33:14,013] [INFO] Task started: CheckM
[2023-06-30 04:33:14,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/checkm_input GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/checkm_result
[2023-06-30 04:33:39,925] [INFO] Task succeeded: CheckM
[2023-06-30 04:33:39,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:33:39,953] [INFO] ===== Completeness check finished =====
[2023-06-30 04:33:39,953] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:33:39,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/markers.fasta)
[2023-06-30 04:33:39,954] [INFO] Task started: Blastn
[2023-06-30 04:33:39,955] [INFO] Running command: blastn -query GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/markers.fasta -db /var/lib/cwl/stg8428b3e6-fcea-44a6-bd45-4efb65f15c34/dqc_reference/reference_markers_gtdb.fasta -out GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:33:41,195] [INFO] Task succeeded: Blastn
[2023-06-30 04:33:41,200] [INFO] Selected 10 target genomes.
[2023-06-30 04:33:41,201] [INFO] Target genome list was writen to GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:33:41,203] [INFO] Task started: fastANI
[2023-06-30 04:33:41,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bb28444-bab8-4036-8339-97117ef086b2/GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna.gz --refList GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/target_genomes_gtdb.txt --output GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:33:47,209] [INFO] Task succeeded: fastANI
[2023-06-30 04:33:47,224] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:33:47,224] [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_903884235.1	s__CAIYLH01 sp903884235	99.057	445	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.42	99.08	0.95	0.88	22	conclusive
GCA_018241525.1	s__SZAS-83 sp018241525	80.6207	262	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903927005.1	s__CAIYLH01 sp903927005	80.5269	248	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.60	99.60	0.92	0.92	2	-
GCA_018241545.1	s__SZAS-83 sp018241545	80.2704	187	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713725.1	s__RPQJ01 sp016713725	78.2349	90	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839465.1	s__CAIKMS01 sp903839465	78.2058	147	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIKMS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003819815.1	s__RPQJ01 sp003819815	78.0846	85	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903890265.1	s__CAIKMS01 sp903890265	77.8677	107	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIKMS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874295.1	s__SCUD01 sp016874295	77.6217	94	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SCUD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:33:47,227] [INFO] GTDB search result was written to GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/result_gtdb.tsv
[2023-06-30 04:33:47,227] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:33:47,231] [INFO] DFAST_QC result json was written to GCA_903865175.1_freshwater_MAG_---_AM5_bin-0311_genomic.fna/dqc_result.json
[2023-06-30 04:33:47,231] [INFO] DFAST_QC completed!
[2023-06-30 04:33:47,231] [INFO] Total running time: 0h0m55s