[2023-06-29 22:11:19,512] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:11:19,516] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:11:19,516] [INFO] DQC Reference Directory: /var/lib/cwl/stg171ce834-d0df-464c-9894-1246d624bb25/dqc_reference
[2023-06-29 22:11:20,785] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:11:20,786] [INFO] Task started: Prodigal
[2023-06-29 22:11:20,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg683636fc-813d-4032-af0c-f479c3d61b85/GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna.gz | prodigal -d GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/cds.fna -a GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:11:25,190] [INFO] Task succeeded: Prodigal
[2023-06-29 22:11:25,191] [INFO] Task started: HMMsearch
[2023-06-29 22:11:25,191] [INFO] Running command: hmmsearch --tblout GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg171ce834-d0df-464c-9894-1246d624bb25/dqc_reference/reference_markers.hmm GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:11:25,414] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:11:25,416] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg683636fc-813d-4032-af0c-f479c3d61b85/GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna.gz]
[2023-06-29 22:11:25,444] [INFO] Query marker FASTA was written to GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/markers.fasta
[2023-06-29 22:11:25,445] [INFO] Task started: Blastn
[2023-06-29 22:11:25,445] [INFO] Running command: blastn -query GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/markers.fasta -db /var/lib/cwl/stg171ce834-d0df-464c-9894-1246d624bb25/dqc_reference/reference_markers.fasta -out GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:11:26,055] [INFO] Task succeeded: Blastn
[2023-06-29 22:11:26,060] [INFO] Selected 20 target genomes.
[2023-06-29 22:11:26,060] [INFO] Target genome list was writen to GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/target_genomes.txt
[2023-06-29 22:11:26,064] [INFO] Task started: fastANI
[2023-06-29 22:11:26,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg683636fc-813d-4032-af0c-f479c3d61b85/GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna.gz --refList GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/target_genomes.txt --output GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:11:38,115] [INFO] Task succeeded: fastANI
[2023-06-29 22:11:38,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg171ce834-d0df-464c-9894-1246d624bb25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:11:38,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg171ce834-d0df-464c-9894-1246d624bb25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:11:38,128] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:11:38,128] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 22:11:38,129] [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
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.8154	60	262	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.8154	60	262	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.2468	60	262	95	below_threshold
Agrococcus terreus	strain=CGMCC 1.6960	GCA_014645235.1	574649	574649	type	True	75.0351	72	262	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	74.7395	69	262	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 22:11:38,131] [INFO] DFAST Taxonomy check result was written to GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/tc_result.tsv
[2023-06-29 22:11:38,132] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:11:38,132] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:11:38,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg171ce834-d0df-464c-9894-1246d624bb25/dqc_reference/checkm_data
[2023-06-29 22:11:38,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:11:38,162] [INFO] Task started: CheckM
[2023-06-29 22:11:38,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/checkm_input GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/checkm_result
[2023-06-29 22:11:57,849] [INFO] Task succeeded: CheckM
[2023-06-29 22:11:57,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:11:57,872] [INFO] ===== Completeness check finished =====
[2023-06-29 22:11:57,873] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:11:57,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/markers.fasta)
[2023-06-29 22:11:57,874] [INFO] Task started: Blastn
[2023-06-29 22:11:57,874] [INFO] Running command: blastn -query GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/markers.fasta -db /var/lib/cwl/stg171ce834-d0df-464c-9894-1246d624bb25/dqc_reference/reference_markers_gtdb.fasta -out GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:11:58,710] [INFO] Task succeeded: Blastn
[2023-06-29 22:11:58,714] [INFO] Selected 11 target genomes.
[2023-06-29 22:11:58,714] [INFO] Target genome list was writen to GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:11:58,749] [INFO] Task started: fastANI
[2023-06-29 22:11:58,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg683636fc-813d-4032-af0c-f479c3d61b85/GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna.gz --refList GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/target_genomes_gtdb.txt --output GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:12:03,541] [INFO] Task succeeded: fastANI
[2023-06-29 22:12:03,553] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 22:12:03,553] [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_016873255.1	s__UBA966 sp016873255	84.5253	214	262	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA966	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883105.1	s__UBA966 sp018883105	82.7535	180	262	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA966	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903867275.1	s__SYAC01 sp903867275	79.0643	60	262	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872835.1	s__SYAC01 sp016872835	78.2565	86	262	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882625.1	s__ZLKRG44 sp018882625	78.1458	80	262	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__ZLKRG44	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924765.1	s__SYAC01 sp009924765	78.0868	63	262	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292895.1	s__UBA966 sp002292895	77.6072	59	262	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA966	95.0	99.22	99.02	0.83	0.82	3	-
GCA_016873355.1	s__VGXK01 sp016873355	77.2717	76	262	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__VGXK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795035.1	s__JAEUIT01 sp016795035	77.0887	98	262	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__JAEUIT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918555.1	s__QWPT01 sp903918555	77.0611	74	262	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 22:12:03,556] [INFO] GTDB search result was written to GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/result_gtdb.tsv
[2023-06-29 22:12:03,557] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:12:03,564] [INFO] DFAST_QC result json was written to GCA_903906105.1_freshwater_MAG_---_LaPlata-5m-b_bin-756_genomic.fna/dqc_result.json
[2023-06-29 22:12:03,564] [INFO] DFAST_QC completed!
[2023-06-29 22:12:03,564] [INFO] Total running time: 0h0m44s