[2023-06-29 14:18:12,939] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:18:12,943] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:18:12,943] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c0de42f-8d99-4e44-9ad1-cb58d996beec/dqc_reference
[2023-06-29 14:18:14,338] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:18:14,339] [INFO] Task started: Prodigal
[2023-06-29 14:18:14,339] [INFO] Running command: gunzip -c /var/lib/cwl/stg99ae7d62-20ac-4657-88ce-6a971ed7af21/GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:18:24,910] [INFO] Task succeeded: Prodigal
[2023-06-29 14:18:24,911] [INFO] Task started: HMMsearch
[2023-06-29 14:18:24,911] [INFO] Running command: hmmsearch --tblout GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c0de42f-8d99-4e44-9ad1-cb58d996beec/dqc_reference/reference_markers.hmm GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:18:25,171] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:18:25,172] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg99ae7d62-20ac-4657-88ce-6a971ed7af21/GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 14:18:25,200] [INFO] Query marker FASTA was written to GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 14:18:25,201] [INFO] Task started: Blastn
[2023-06-29 14:18:25,201] [INFO] Running command: blastn -query GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c0de42f-8d99-4e44-9ad1-cb58d996beec/dqc_reference/reference_markers.fasta -out GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:18:25,839] [INFO] Task succeeded: Blastn
[2023-06-29 14:18:25,843] [INFO] Selected 25 target genomes.
[2023-06-29 14:18:25,843] [INFO] Target genome list was writen to GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 14:18:25,847] [INFO] Task started: fastANI
[2023-06-29 14:18:25,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg99ae7d62-20ac-4657-88ce-6a971ed7af21/GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:18:40,130] [INFO] Task succeeded: fastANI
[2023-06-29 14:18:40,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c0de42f-8d99-4e44-9ad1-cb58d996beec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:18:40,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c0de42f-8d99-4e44-9ad1-cb58d996beec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:18:40,141] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:18:40,141] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:18:40,141] [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
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	77.4034	169	633	95	below_threshold
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	76.8121	59	633	95	below_threshold
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	76.4451	84	633	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	76.3205	67	633	95	below_threshold
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	76.2752	59	633	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	76.2672	68	633	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	76.1597	75	633	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.0224	53	633	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:18:40,143] [INFO] DFAST Taxonomy check result was written to GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 14:18:40,144] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:18:40,144] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:18:40,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c0de42f-8d99-4e44-9ad1-cb58d996beec/dqc_reference/checkm_data
[2023-06-29 14:18:40,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:18:40,177] [INFO] Task started: CheckM
[2023-06-29 14:18:40,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 14:19:14,287] [INFO] Task succeeded: CheckM
[2023-06-29 14:19:14,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:19:14,311] [INFO] ===== Completeness check finished =====
[2023-06-29 14:19:14,311] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:19:14,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 14:19:14,312] [INFO] Task started: Blastn
[2023-06-29 14:19:14,312] [INFO] Running command: blastn -query GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c0de42f-8d99-4e44-9ad1-cb58d996beec/dqc_reference/reference_markers_gtdb.fasta -out GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:19:15,181] [INFO] Task succeeded: Blastn
[2023-06-29 14:19:15,186] [INFO] Selected 23 target genomes.
[2023-06-29 14:19:15,186] [INFO] Target genome list was writen to GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:19:15,216] [INFO] Task started: fastANI
[2023-06-29 14:19:15,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg99ae7d62-20ac-4657-88ce-6a971ed7af21/GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:19:26,979] [INFO] Task succeeded: fastANI
[2023-06-29 14:19:26,996] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:19:26,996] [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_002707025.1	s__IN17 sp002707025	99.8913	629	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.83	99.78	0.96	0.93	3	conclusive
GCA_002694465.1	s__IN17 sp002694465	77.2967	169	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	-
GCA_013002065.1	s__SMXJ01 sp013002065	77.0275	88	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	76.8384	75	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813135.1	s__Altibacter sp002813135	76.6823	81	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375495.1	s__Marinirhabdus sp002375495	76.6634	77	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCA_002440705.1	s__IN17 sp002440705	76.5696	136	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.92	99.92	0.93	0.93	2	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	76.4944	62	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002379985.1	s__Marixanthomonas sp002379985	76.4896	75	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	99.95	99.94	0.93	0.86	4	-
GCA_002360635.1	s__Marixanthomonas sp002360635	76.3766	87	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCA_011044175.1	s__Marinirhabdus sp011044175	76.3718	61	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003413745.1	s__Marixanthomonas ophiurae	76.2945	67	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900489465.1	s__Aequorivita sp900489465	76.2013	53	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346335.1	s__Aequorivita sinensis	76.0529	52	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2023-06-29 14:19:26,998] [INFO] GTDB search result was written to GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 14:19:26,999] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:19:27,002] [INFO] DFAST_QC result json was written to GCA_937901205.1_ERR598960_bin.1_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 14:19:27,003] [INFO] DFAST_QC completed!
[2023-06-29 14:19:27,003] [INFO] Total running time: 0h1m14s