[2023-06-30 18:31:46,452] [INFO] DFAST_QC pipeline started.
[2023-06-30 18:31:46,465] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 18:31:46,465] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ed571d8-d715-4b1c-9ffd-3c6a9444d37b/dqc_reference
[2023-06-30 18:31:49,260] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 18:31:49,261] [INFO] Task started: Prodigal
[2023-06-30 18:31:49,261] [INFO] Running command: gunzip -c /var/lib/cwl/stg790feb6d-e88d-494f-9240-29af6c42ca09/GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna.gz | prodigal -d GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/cds.fna -a GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 18:31:53,590] [INFO] Task succeeded: Prodigal
[2023-06-30 18:31:53,590] [INFO] Task started: HMMsearch
[2023-06-30 18:31:53,590] [INFO] Running command: hmmsearch --tblout GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ed571d8-d715-4b1c-9ffd-3c6a9444d37b/dqc_reference/reference_markers.hmm GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/protein.faa > /dev/null
[2023-06-30 18:31:53,792] [INFO] Task succeeded: HMMsearch
[2023-06-30 18:31:53,793] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg790feb6d-e88d-494f-9240-29af6c42ca09/GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna.gz]
[2023-06-30 18:31:53,826] [INFO] Query marker FASTA was written to GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/markers.fasta
[2023-06-30 18:31:53,827] [INFO] Task started: Blastn
[2023-06-30 18:31:53,827] [INFO] Running command: blastn -query GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ed571d8-d715-4b1c-9ffd-3c6a9444d37b/dqc_reference/reference_markers.fasta -out GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:31:55,222] [INFO] Task succeeded: Blastn
[2023-06-30 18:31:55,226] [INFO] Selected 17 target genomes.
[2023-06-30 18:31:55,226] [INFO] Target genome list was writen to GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/target_genomes.txt
[2023-06-30 18:31:55,252] [INFO] Task started: fastANI
[2023-06-30 18:31:55,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg790feb6d-e88d-494f-9240-29af6c42ca09/GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna.gz --refList GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/target_genomes.txt --output GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 18:32:07,733] [INFO] Task succeeded: fastANI
[2023-06-30 18:32:07,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ed571d8-d715-4b1c-9ffd-3c6a9444d37b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 18:32:07,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ed571d8-d715-4b1c-9ffd-3c6a9444d37b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 18:32:07,740] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 18:32:07,741] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 18:32:07,741] [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
Pelobacter propionicus	strain=DSM 2379	GCA_000015045.1	29543	29543	type	True	77.3028	52	284	95	below_threshold
Oryzomonas rubra	strain=Red88	GCA_008369015.1	2509454	2509454	type	True	77.2419	62	284	95	below_threshold
Oryzomonas sagensis	strain=Red100	GCA_008802355.1	2603857	2603857	type	True	77.0519	62	284	95	below_threshold
Oryzomonas japonica	strain=Red96	GCA_008802365.1	2603858	2603858	type	True	76.9143	58	284	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 18:32:07,744] [INFO] DFAST Taxonomy check result was written to GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/tc_result.tsv
[2023-06-30 18:32:07,745] [INFO] ===== Taxonomy check completed =====
[2023-06-30 18:32:07,745] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 18:32:07,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ed571d8-d715-4b1c-9ffd-3c6a9444d37b/dqc_reference/checkm_data
[2023-06-30 18:32:07,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 18:32:07,782] [INFO] Task started: CheckM
[2023-06-30 18:32:07,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/checkm_input GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/checkm_result
[2023-06-30 18:32:29,360] [INFO] Task succeeded: CheckM
[2023-06-30 18:32:29,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.68%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 18:32:29,379] [INFO] ===== Completeness check finished =====
[2023-06-30 18:32:29,379] [INFO] ===== Start GTDB Search =====
[2023-06-30 18:32:29,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/markers.fasta)
[2023-06-30 18:32:29,380] [INFO] Task started: Blastn
[2023-06-30 18:32:29,380] [INFO] Running command: blastn -query GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ed571d8-d715-4b1c-9ffd-3c6a9444d37b/dqc_reference/reference_markers_gtdb.fasta -out GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:32:29,930] [INFO] Task succeeded: Blastn
[2023-06-30 18:32:29,933] [INFO] Selected 13 target genomes.
[2023-06-30 18:32:29,933] [INFO] Target genome list was writen to GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 18:32:29,936] [INFO] Task started: fastANI
[2023-06-30 18:32:29,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg790feb6d-e88d-494f-9240-29af6c42ca09/GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna.gz --refList GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/target_genomes_gtdb.txt --output GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 18:32:37,825] [INFO] Task succeeded: fastANI
[2023-06-30 18:32:37,844] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 18:32:37,845] [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_903852495.1	s__JACRCG01 sp903852495	99.7623	279	284	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	99.47	98.75	0.91	0.82	26	conclusive
GCA_903862245.1	s__JACRCG01 sp903862245	88.4247	243	284	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	99.89	99.85	0.93	0.90	4	-
GCA_009886055.1	s__JACRCG01 sp009886055	79.4966	137	284	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903925005.1	s__JACRCG01 sp903925005	78.4929	132	284	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	99.76	99.70	0.93	0.92	4	-
GCA_019162745.1	s__JACRCG01 sp019162745	78.298	130	284	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885845.1	s__JACRCG01 sp009885845	78.1191	114	284	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001802645.1	s__JACRCG01 sp001802645	78.0375	129	284	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013336525.1	s__JACRCG01 sp013336525	77.8163	109	284	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	99.96	99.96	0.98	0.98	2	-
GCA_013349405.1	s__JACRCG01 sp013349405	77.7642	93	284	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875605.1	s__JACRCG01 sp903875605	77.4585	100	284	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	99.93	99.90	0.94	0.93	3	-
GCA_001802125.1	s__JACRCG01 sp001802125	77.4531	73	284	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	99.79	99.67	0.87	0.84	4	-
GCA_903879825.1	s__JACRCG01 sp903879825	76.8874	91	284	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 18:32:37,847] [INFO] GTDB search result was written to GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/result_gtdb.tsv
[2023-06-30 18:32:37,848] [INFO] ===== GTDB Search completed =====
[2023-06-30 18:32:37,852] [INFO] DFAST_QC result json was written to GCA_903852515.1_freshwater_MAG_---_MJ120730B_bin-100_genomic.fna/dqc_result.json
[2023-06-30 18:32:37,852] [INFO] DFAST_QC completed!
[2023-06-30 18:32:37,852] [INFO] Total running time: 0h0m51s