[2023-06-19 04:44:12,352] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:44:12,354] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:44:12,354] [INFO] DQC Reference Directory: /var/lib/cwl/stga148f22c-5ae0-4cd1-a4de-f673c47bd90b/dqc_reference
[2023-06-19 04:44:13,688] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:44:13,689] [INFO] Task started: Prodigal
[2023-06-19 04:44:13,689] [INFO] Running command: gunzip -c /var/lib/cwl/stg7837f746-9238-4491-8ada-ea574f2365f0/GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:44:28,654] [INFO] Task succeeded: Prodigal
[2023-06-19 04:44:28,655] [INFO] Task started: HMMsearch
[2023-06-19 04:44:28,655] [INFO] Running command: hmmsearch --tblout GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga148f22c-5ae0-4cd1-a4de-f673c47bd90b/dqc_reference/reference_markers.hmm GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:44:29,000] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:44:29,001] [INFO] Found 6/6 markers.
[2023-06-19 04:44:29,066] [INFO] Query marker FASTA was written to GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 04:44:29,066] [INFO] Task started: Blastn
[2023-06-19 04:44:29,066] [INFO] Running command: blastn -query GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga148f22c-5ae0-4cd1-a4de-f673c47bd90b/dqc_reference/reference_markers.fasta -out GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:44:29,694] [INFO] Task succeeded: Blastn
[2023-06-19 04:44:29,698] [INFO] Selected 24 target genomes.
[2023-06-19 04:44:29,699] [INFO] Target genome list was writen to GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 04:44:29,701] [INFO] Task started: fastANI
[2023-06-19 04:44:29,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg7837f746-9238-4491-8ada-ea574f2365f0/GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:44:46,092] [INFO] Task succeeded: fastANI
[2023-06-19 04:44:46,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga148f22c-5ae0-4cd1-a4de-f673c47bd90b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:44:46,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga148f22c-5ae0-4cd1-a4de-f673c47bd90b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:44:46,101] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:44:46,102] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 04:44:46,102] [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
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	76.6755	270	1598	95	below_threshold
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	76.178	110	1598	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	76.0419	109	1598	95	below_threshold
Gemmatimonas phototrophica	strain=AP64	GCA_000695095.2	1379270	1379270	type	True	76.0283	90	1598	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.4511	107	1598	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.4373	111	1598	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	74.8874	86	1598	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	74.6765	57	1598	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 04:44:46,107] [INFO] DFAST Taxonomy check result was written to GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 04:44:46,108] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:44:46,108] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:44:46,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga148f22c-5ae0-4cd1-a4de-f673c47bd90b/dqc_reference/checkm_data
[2023-06-19 04:44:46,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:44:46,162] [INFO] Task started: CheckM
[2023-06-19 04:44:46,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 04:45:31,116] [INFO] Task succeeded: CheckM
[2023-06-19 04:45:31,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:45:31,174] [INFO] ===== Completeness check finished =====
[2023-06-19 04:45:31,174] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:45:31,174] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 04:45:31,175] [INFO] Task started: Blastn
[2023-06-19 04:45:31,175] [INFO] Running command: blastn -query GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga148f22c-5ae0-4cd1-a4de-f673c47bd90b/dqc_reference/reference_markers_gtdb.fasta -out GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:45:32,174] [INFO] Task succeeded: Blastn
[2023-06-19 04:45:32,179] [INFO] Selected 26 target genomes.
[2023-06-19 04:45:32,180] [INFO] Target genome list was writen to GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:45:32,190] [INFO] Task started: fastANI
[2023-06-19 04:45:32,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg7837f746-9238-4491-8ada-ea574f2365f0/GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:45:49,761] [INFO] Task succeeded: fastANI
[2023-06-19 04:45:49,784] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 04:45:49,784] [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_016194585.1	s__Fen-1231 sp016194585	76.8611	151	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	99.33	99.33	0.81	0.81	2	-
GCA_013361935.1	s__JABFXC01 sp013361935	76.7824	183	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01	95.0	99.88	99.88	0.94	0.92	3	-
GCF_000522985.1	s__Gemmatirosa kalamazoonesis	76.718	266	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatirosa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714015.1	s__PNKF01 sp016714015	76.7157	175	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361335.1	s__AG11 sp013361335	76.6942	182	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	99.60	99.48	0.90	0.83	7	-
GCA_016191225.1	s__JACPPC01 sp016191225	76.599	173	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JACPPC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223455.1	s__AG11 sp003223455	76.582	165	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825965.1	s__PNKF01 sp902825965	76.5534	159	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361745.1	s__JABFXC01 sp013361745	76.5477	112	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218305.1	s__PNKL01 sp016218305	76.524	97	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724275.1	s__SCN-70-22 sp001724275	76.4631	174	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__SCN-70-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704465.1	s__SCN-70-22 sp016704465	76.4592	169	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__SCN-70-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871855.1	s__PNKL01 sp016871855	76.4318	114	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719105.1	s__SCN-70-22 sp016719105	76.356	197	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__SCN-70-22	95.0	98.70	98.52	0.93	0.89	8	-
GCA_903910555.1	s__Fen-1231 sp903910555	76.3439	71	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	99.81	99.24	0.99	0.96	5	-
GCA_003171215.1	s__Fen-1231 sp003171215	76.3377	131	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	97.59	95.49	0.88	0.84	3	-
GCA_903876745.1	s__Fen-1231 sp903876745	76.1624	73	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816855.1	s__UBA4720 sp013816855	76.1591	54	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__UBA4720	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390935.1	s__JAABRT01 sp011390935	76.0755	117	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JAABRT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794835.1	s__SCN-70-22 sp016794835	75.9085	102	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__SCN-70-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003142495.1	s__FEN-1250 sp003142495	75.719	84	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__FEN-1250	95.0	97.40	97.40	0.82	0.82	2	-
GCA_017991005.1	s__Gemmatimonas sp017991005	75.6124	73	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222085.1	s__AG41 sp003222085	75.5526	63	1598	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG41	95.0	99.39	98.99	0.94	0.93	4	-
--------------------------------------------------------------------------------
[2023-06-19 04:45:49,787] [INFO] GTDB search result was written to GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 04:45:49,787] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:45:49,791] [INFO] DFAST_QC result json was written to GCA_937906875.1_SRR3997477_bin.119_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 04:45:49,791] [INFO] DFAST_QC completed!
[2023-06-19 04:45:49,791] [INFO] Total running time: 0h1m37s