[2023-06-29 21:20:24,017] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:20:24,019] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:20:24,020] [INFO] DQC Reference Directory: /var/lib/cwl/stg91a10380-3e04-4a4a-8af0-aacf2ec473b3/dqc_reference
[2023-06-29 21:20:25,252] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:20:25,253] [INFO] Task started: Prodigal
[2023-06-29 21:20:25,253] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e6c99c8-06ce-408e-a11b-49281f6f9049/GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna.gz | prodigal -d GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/cds.fna -a GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:20:38,552] [INFO] Task succeeded: Prodigal
[2023-06-29 21:20:38,552] [INFO] Task started: HMMsearch
[2023-06-29 21:20:38,553] [INFO] Running command: hmmsearch --tblout GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91a10380-3e04-4a4a-8af0-aacf2ec473b3/dqc_reference/reference_markers.hmm GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:20:38,774] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:20:38,775] [INFO] Found 6/6 markers.
[2023-06-29 21:20:38,808] [INFO] Query marker FASTA was written to GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/markers.fasta
[2023-06-29 21:20:38,809] [INFO] Task started: Blastn
[2023-06-29 21:20:38,809] [INFO] Running command: blastn -query GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/markers.fasta -db /var/lib/cwl/stg91a10380-3e04-4a4a-8af0-aacf2ec473b3/dqc_reference/reference_markers.fasta -out GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:20:39,587] [INFO] Task succeeded: Blastn
[2023-06-29 21:20:39,591] [INFO] Selected 23 target genomes.
[2023-06-29 21:20:39,592] [INFO] Target genome list was writen to GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/target_genomes.txt
[2023-06-29 21:20:39,598] [INFO] Task started: fastANI
[2023-06-29 21:20:39,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e6c99c8-06ce-408e-a11b-49281f6f9049/GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna.gz --refList GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/target_genomes.txt --output GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:20:57,391] [INFO] Task succeeded: fastANI
[2023-06-29 21:20:57,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91a10380-3e04-4a4a-8af0-aacf2ec473b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:20:57,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91a10380-3e04-4a4a-8af0-aacf2ec473b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:20:57,409] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:20:57,409] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:20:57,409] [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
Nevskia soli	strain=DSM 19509	GCA_000711955.1	418856	418856	type	True	78.5561	511	1478	95	below_threshold
Nevskia ramosa	strain=DSM 11499	GCA_000420645.1	64002	64002	type	True	78.4962	446	1478	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	78.1746	402	1478	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	78.0598	434	1478	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	78.0008	442	1478	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	77.9877	354	1478	95	below_threshold
Hydrocarboniphaga daqingensis	strain=CGMCC 1.7049	GCA_900129825.1	490188	490188	type	True	77.7798	335	1478	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004799025.1	381431	381431	type	True	77.5995	346	1478	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004364935.1	381431	381431	type	True	77.5765	356	1478	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	76.9109	182	1478	95	below_threshold
Stenotrophobium rhamnosiphilum	strain=GT1R17	GCA_003052265.1	2029166	2029166	type	True	76.4189	149	1478	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	76.0286	133	1478	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.017	158	1478	95	below_threshold
Pseudomonas vancouverensis	strain=CCUG 49675	GCA_008801375.1	95300	95300	type	True	75.9591	81	1478	95	below_threshold
Pseudomonas azerbaijanoccidens	strain=SWRI74	GCA_019145495.1	2842347	2842347	type	True	75.7069	83	1478	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	75.6131	104	1478	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	75.5701	99	1478	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	75.498	105	1478	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	75.4887	106	1478	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	75.4804	107	1478	95	below_threshold
Acidihalobacter ferrooxydans	strain=V8	GCA_001975725.1	1765967	1765967	type	True	75.4622	72	1478	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	75.4542	103	1478	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	75.2826	90	1478	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:20:57,411] [INFO] DFAST Taxonomy check result was written to GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/tc_result.tsv
[2023-06-29 21:20:57,412] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:20:57,412] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:20:57,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91a10380-3e04-4a4a-8af0-aacf2ec473b3/dqc_reference/checkm_data
[2023-06-29 21:20:57,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:20:57,455] [INFO] Task started: CheckM
[2023-06-29 21:20:57,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/checkm_input GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/checkm_result
[2023-06-29 21:21:37,950] [INFO] Task succeeded: CheckM
[2023-06-29 21:21:37,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:21:37,969] [INFO] ===== Completeness check finished =====
[2023-06-29 21:21:37,969] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:21:37,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/markers.fasta)
[2023-06-29 21:21:37,970] [INFO] Task started: Blastn
[2023-06-29 21:21:37,970] [INFO] Running command: blastn -query GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/markers.fasta -db /var/lib/cwl/stg91a10380-3e04-4a4a-8af0-aacf2ec473b3/dqc_reference/reference_markers_gtdb.fasta -out GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:21:39,396] [INFO] Task succeeded: Blastn
[2023-06-29 21:21:39,400] [INFO] Selected 12 target genomes.
[2023-06-29 21:21:39,400] [INFO] Target genome list was writen to GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:21:39,407] [INFO] Task started: fastANI
[2023-06-29 21:21:39,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e6c99c8-06ce-408e-a11b-49281f6f9049/GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna.gz --refList GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/target_genomes_gtdb.txt --output GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:21:48,976] [INFO] Task succeeded: fastANI
[2023-06-29 21:21:48,987] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:21:48,987] [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_903822975.1	s__Nevskia sp903822975	100.0	1477	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCA_903970615.1	s__Nevskia sp903970615	80.2854	608	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779605.1	s__Nevskia sp016779605	78.5483	395	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711955.1	s__Nevskia soli	78.5416	514	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420645.1	s__Nevskia ramosa	78.4992	445	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885465.1	s__Nevskia sp903885465	78.2918	373	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823855.1	s__Nevskia sp013823855	78.2532	395	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271305.1	s__Hydrocarboniphaga effusa	77.9967	353	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970595.1	s__Nevskia sp903970595	77.9076	389	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129825.1	s__Hydrocarboniphaga daqingensis	77.7604	337	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730135.1	s__Stagnimonas aquatica	77.518	326	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297005.1	s__Stagnimonas sp004297005	77.3995	303	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	99.89	99.89	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-29 21:21:48,989] [INFO] GTDB search result was written to GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/result_gtdb.tsv
[2023-06-29 21:21:48,990] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:21:48,994] [INFO] DFAST_QC result json was written to GCA_903822975.1_freshwater_MAG_---_MJ130729B_bin-348_genomic.fna/dqc_result.json
[2023-06-29 21:21:48,994] [INFO] DFAST_QC completed!
[2023-06-29 21:21:48,994] [INFO] Total running time: 0h1m25s