[2023-06-28 14:19:40,274] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:19:40,276] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:19:40,277] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7873eed-3760-4d2d-9d81-0a399fa7ce13/dqc_reference
[2023-06-28 14:19:41,494] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:19:41,495] [INFO] Task started: Prodigal
[2023-06-28 14:19:41,495] [INFO] Running command: gunzip -c /var/lib/cwl/stgf84bf688-4e89-497b-9bb9-c958e4ae675a/GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:20:23,013] [INFO] Task succeeded: Prodigal
[2023-06-28 14:20:23,014] [INFO] Task started: HMMsearch
[2023-06-28 14:20:23,014] [INFO] Running command: hmmsearch --tblout GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7873eed-3760-4d2d-9d81-0a399fa7ce13/dqc_reference/reference_markers.hmm GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:20:23,301] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:20:23,302] [INFO] Found 6/6 markers.
[2023-06-28 14:20:23,357] [INFO] Query marker FASTA was written to GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 14:20:23,357] [INFO] Task started: Blastn
[2023-06-28 14:20:23,357] [INFO] Running command: blastn -query GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7873eed-3760-4d2d-9d81-0a399fa7ce13/dqc_reference/reference_markers.fasta -out GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:20:23,938] [INFO] Task succeeded: Blastn
[2023-06-28 14:20:23,942] [INFO] Selected 30 target genomes.
[2023-06-28 14:20:23,942] [INFO] Target genome list was writen to GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 14:20:23,944] [INFO] Task started: fastANI
[2023-06-28 14:20:23,944] [INFO] Running command: fastANI --query /var/lib/cwl/stgf84bf688-4e89-497b-9bb9-c958e4ae675a/GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:20:44,944] [INFO] Task succeeded: fastANI
[2023-06-28 14:20:44,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7873eed-3760-4d2d-9d81-0a399fa7ce13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:20:44,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7873eed-3760-4d2d-9d81-0a399fa7ce13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:20:44,957] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:20:44,957] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 14:20:44,957] [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
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.7112	70	1975	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	75.4922	57	1975	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.1464	60	1975	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	75.1436	69	1975	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.0039	107	1975	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.9596	102	1975	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	74.8572	54	1975	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	74.8378	55	1975	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	74.837	56	1975	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	74.6477	54	1975	95	below_threshold
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	74.609	81	1975	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 14:20:44,959] [INFO] DFAST Taxonomy check result was written to GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 14:20:44,961] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:20:44,961] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:20:44,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7873eed-3760-4d2d-9d81-0a399fa7ce13/dqc_reference/checkm_data
[2023-06-28 14:20:44,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:20:45,032] [INFO] Task started: CheckM
[2023-06-28 14:20:45,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 14:22:29,624] [INFO] Task succeeded: CheckM
[2023-06-28 14:22:29,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:22:29,649] [INFO] ===== Completeness check finished =====
[2023-06-28 14:22:29,650] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:22:29,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 14:22:29,652] [INFO] Task started: Blastn
[2023-06-28 14:22:29,653] [INFO] Running command: blastn -query GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7873eed-3760-4d2d-9d81-0a399fa7ce13/dqc_reference/reference_markers_gtdb.fasta -out GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:22:30,493] [INFO] Task succeeded: Blastn
[2023-06-28 14:22:30,498] [INFO] Selected 15 target genomes.
[2023-06-28 14:22:30,499] [INFO] Target genome list was writen to GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:22:30,501] [INFO] Task started: fastANI
[2023-06-28 14:22:30,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgf84bf688-4e89-497b-9bb9-c958e4ae675a/GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:22:42,380] [INFO] Task succeeded: fastANI
[2023-06-28 14:22:42,389] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 14:22:42,390] [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_002862085.1	s__GCA-2862085 sp002862085	78.6363	409	1975	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779205.1	s__GCA-2862085 sp016779205	77.8659	354	1975	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007751475.1	s__GCA-2862085 sp007751475	77.8461	441	1975	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480285.1	s__GCA-2862085 sp905480285	77.4493	301	1975	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524785.1	s__GCA-2686945 sp011524785	76.7745	120	1975	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686945	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720975.1	s__GCA-2720975 sp002720975	76.1805	71	1975	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2720975	95.0	96.24	96.24	0.74	0.74	2	-
GCA_016712565.1	s__JADJQU01 sp016712565	75.9667	130	1975	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJQU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	75.9627	113	1975	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004357655.1	s__N075bin59 sp004357655	75.9593	131	1975	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__N075bin59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686265.1	s__GCA-2686265 sp002686265	75.7918	125	1975	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686265	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709545.1	s__JADJMO01 sp016709545	74.919	116	1975	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JADJMO01;g__JADJMO01	95.0	95.09	95.09	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-28 14:22:42,392] [INFO] GTDB search result was written to GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 14:22:42,392] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:22:42,395] [INFO] DFAST_QC result json was written to GCA_913058555.1_SRR3933245_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 14:22:42,396] [INFO] DFAST_QC completed!
[2023-06-28 14:22:42,396] [INFO] Total running time: 0h3m2s