[2023-07-01 04:06:03,256] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:06:03,258] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:06:03,258] [INFO] DQC Reference Directory: /var/lib/cwl/stg095b7a21-d1da-4a8c-abff-2fff5df02487/dqc_reference
[2023-07-01 04:06:04,562] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:06:04,563] [INFO] Task started: Prodigal
[2023-07-01 04:06:04,564] [INFO] Running command: gunzip -c /var/lib/cwl/stgce0b1d6e-aec8-4c04-b4db-a2e3192c294b/GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna.gz | prodigal -d GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/cds.fna -a GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:06:19,716] [INFO] Task succeeded: Prodigal
[2023-07-01 04:06:19,717] [INFO] Task started: HMMsearch
[2023-07-01 04:06:19,717] [INFO] Running command: hmmsearch --tblout GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg095b7a21-d1da-4a8c-abff-2fff5df02487/dqc_reference/reference_markers.hmm GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:06:19,984] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:06:19,985] [INFO] Found 6/6 markers.
[2023-07-01 04:06:20,028] [INFO] Query marker FASTA was written to GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/markers.fasta
[2023-07-01 04:06:20,028] [INFO] Task started: Blastn
[2023-07-01 04:06:20,028] [INFO] Running command: blastn -query GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/markers.fasta -db /var/lib/cwl/stg095b7a21-d1da-4a8c-abff-2fff5df02487/dqc_reference/reference_markers.fasta -out GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:06:20,606] [INFO] Task succeeded: Blastn
[2023-07-01 04:06:20,609] [INFO] Selected 27 target genomes.
[2023-07-01 04:06:20,609] [INFO] Target genome list was writen to GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/target_genomes.txt
[2023-07-01 04:06:20,612] [INFO] Task started: fastANI
[2023-07-01 04:06:20,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgce0b1d6e-aec8-4c04-b4db-a2e3192c294b/GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna.gz --refList GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/target_genomes.txt --output GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:06:36,114] [INFO] Task succeeded: fastANI
[2023-07-01 04:06:36,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg095b7a21-d1da-4a8c-abff-2fff5df02487/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:06:36,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg095b7a21-d1da-4a8c-abff-2fff5df02487/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:06:36,118] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:06:36,118] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 04:06:36,118] [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
Longilinea arvoryzae	strain=KOME-1	GCA_001050235.2	360412	360412	type	True	75.5708	56	1749	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 04:06:36,120] [INFO] DFAST Taxonomy check result was written to GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/tc_result.tsv
[2023-07-01 04:06:36,120] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:06:36,121] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:06:36,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg095b7a21-d1da-4a8c-abff-2fff5df02487/dqc_reference/checkm_data
[2023-07-01 04:06:36,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:06:36,170] [INFO] Task started: CheckM
[2023-07-01 04:06:36,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/checkm_input GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/checkm_result
[2023-07-01 04:07:22,326] [INFO] Task succeeded: CheckM
[2023-07-01 04:07:22,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 04:07:22,342] [INFO] ===== Completeness check finished =====
[2023-07-01 04:07:22,343] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:07:22,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/markers.fasta)
[2023-07-01 04:07:22,343] [INFO] Task started: Blastn
[2023-07-01 04:07:22,343] [INFO] Running command: blastn -query GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/markers.fasta -db /var/lib/cwl/stg095b7a21-d1da-4a8c-abff-2fff5df02487/dqc_reference/reference_markers_gtdb.fasta -out GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:07:23,148] [INFO] Task succeeded: Blastn
[2023-07-01 04:07:23,152] [INFO] Selected 19 target genomes.
[2023-07-01 04:07:23,152] [INFO] Target genome list was writen to GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:07:23,158] [INFO] Task started: fastANI
[2023-07-01 04:07:23,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgce0b1d6e-aec8-4c04-b4db-a2e3192c294b/GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna.gz --refList GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/target_genomes_gtdb.txt --output GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:07:36,972] [INFO] Task succeeded: fastANI
[2023-07-01 04:07:36,985] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 04:07:36,985] [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_903838415.1	s__UBA5195 sp903838415	99.9058	1611	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5195	95.0	99.77	99.48	0.94	0.90	22	conclusive
GCA_903875215.1	s__UBA5195 sp903875215	80.5466	410	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5195	95.0	99.98	99.95	0.99	0.97	6	-
GCA_903846015.1	s__UBA5195 sp903846015	78.6436	311	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5195	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002412925.1	s__UBA5195 sp002412925	78.2106	497	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5195	95.0	99.92	99.92	0.94	0.94	2	-
GCA_903854805.1	s__UBA5195 sp903854805	78.1882	330	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5195	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908605.1	s__UBA5195 sp903908605	77.7199	255	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5195	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903910795.1	s__UBA5195 sp903910795	77.3944	260	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5195	95.0	99.82	99.82	0.91	0.91	2	-
GCA_903822545.1	s__CAIJPN01 sp903822545	77.3925	312	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__CAIJPN01	95.0	99.95	99.94	0.96	0.96	6	-
GCA_002840685.1	s__UBA8950 sp002840685	76.9591	241	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA8950	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011047105.1	s__UBA5195 sp011047105	76.696	225	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5195	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152325.1	s__Desulfolinea sp013152325	75.8548	106	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002473085.1	s__UBA7227 sp002473085	75.8529	83	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA7227	95.0	98.42	98.07	0.85	0.72	10	-
GCA_011367945.1	s__DSXF01 sp011367945	75.7351	65	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__DSXF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721115.1	s__UBA12294 sp016721115	75.628	55	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885525.1	s__OLB14 sp009885525	75.5313	77	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903829085.1	s__UBA877 sp903829085	75.499	54	1749	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 04:07:36,987] [INFO] GTDB search result was written to GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/result_gtdb.tsv
[2023-07-01 04:07:36,987] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:07:36,991] [INFO] DFAST_QC result json was written to GCA_903907145.1_freshwater_MAG_---_KTt_bin-0300_genomic.fna/dqc_result.json
[2023-07-01 04:07:36,991] [INFO] DFAST_QC completed!
[2023-07-01 04:07:36,991] [INFO] Total running time: 0h1m34s