[2023-06-30 00:55:15,176] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:55:15,179] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:55:15,179] [INFO] DQC Reference Directory: /var/lib/cwl/stgad55e1f8-458a-4627-bbd4-6b2587a3f9e5/dqc_reference
[2023-06-30 00:55:16,496] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:55:16,497] [INFO] Task started: Prodigal
[2023-06-30 00:55:16,498] [INFO] Running command: gunzip -c /var/lib/cwl/stg6282c1a4-fa5d-4d12-a266-cdcb5f19ce75/GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna.gz | prodigal -d GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/cds.fna -a GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:55:29,379] [INFO] Task succeeded: Prodigal
[2023-06-30 00:55:29,380] [INFO] Task started: HMMsearch
[2023-06-30 00:55:29,380] [INFO] Running command: hmmsearch --tblout GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad55e1f8-458a-4627-bbd4-6b2587a3f9e5/dqc_reference/reference_markers.hmm GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:55:29,636] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:55:29,637] [INFO] Found 6/6 markers.
[2023-06-30 00:55:29,662] [INFO] Query marker FASTA was written to GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/markers.fasta
[2023-06-30 00:55:29,662] [INFO] Task started: Blastn
[2023-06-30 00:55:29,662] [INFO] Running command: blastn -query GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/markers.fasta -db /var/lib/cwl/stgad55e1f8-458a-4627-bbd4-6b2587a3f9e5/dqc_reference/reference_markers.fasta -out GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:55:30,340] [INFO] Task succeeded: Blastn
[2023-06-30 00:55:30,344] [INFO] Selected 23 target genomes.
[2023-06-30 00:55:30,344] [INFO] Target genome list was writen to GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/target_genomes.txt
[2023-06-30 00:55:30,348] [INFO] Task started: fastANI
[2023-06-30 00:55:30,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg6282c1a4-fa5d-4d12-a266-cdcb5f19ce75/GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna.gz --refList GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/target_genomes.txt --output GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:55:47,589] [INFO] Task succeeded: fastANI
[2023-06-30 00:55:47,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad55e1f8-458a-4627-bbd4-6b2587a3f9e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:55:47,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad55e1f8-458a-4627-bbd4-6b2587a3f9e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:55:47,591] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:55:47,591] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 00:55:47,591] [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
--------------------------------------------------------------------------------
[2023-06-30 00:55:47,598] [INFO] DFAST Taxonomy check result was written to GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/tc_result.tsv
[2023-06-30 00:55:47,598] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:55:47,599] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:55:47,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad55e1f8-458a-4627-bbd4-6b2587a3f9e5/dqc_reference/checkm_data
[2023-06-30 00:55:47,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:55:47,634] [INFO] Task started: CheckM
[2023-06-30 00:55:47,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/checkm_input GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/checkm_result
[2023-06-30 00:56:25,995] [INFO] Task succeeded: CheckM
[2023-06-30 00:56:25,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:56:26,018] [INFO] ===== Completeness check finished =====
[2023-06-30 00:56:26,019] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:56:26,020] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/markers.fasta)
[2023-06-30 00:56:26,020] [INFO] Task started: Blastn
[2023-06-30 00:56:26,020] [INFO] Running command: blastn -query GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/markers.fasta -db /var/lib/cwl/stgad55e1f8-458a-4627-bbd4-6b2587a3f9e5/dqc_reference/reference_markers_gtdb.fasta -out GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:56:26,931] [INFO] Task succeeded: Blastn
[2023-06-30 00:56:26,936] [INFO] Selected 15 target genomes.
[2023-06-30 00:56:26,936] [INFO] Target genome list was writen to GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:56:26,939] [INFO] Task started: fastANI
[2023-06-30 00:56:26,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg6282c1a4-fa5d-4d12-a266-cdcb5f19ce75/GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna.gz --refList GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/target_genomes_gtdb.txt --output GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:56:33,875] [INFO] Task succeeded: fastANI
[2023-06-30 00:56:33,894] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 00:56:33,894] [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_903829855.1	s__UBA953 sp903829855	99.699	513	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.27	99.00	0.85	0.74	14	conclusive
GCA_903889525.1	s__UBA953 sp903889525	90.5834	471	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903855995.1	s__UBA953 sp903855995	83.6932	447	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.61	99.32	0.98	0.94	20	-
GCA_003569165.1	s__UBA953 sp003569165	81.575	329	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293385.1	s__UBA953 sp004293385	81.5432	178	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924535.1	s__UBA953 sp009924535	81.3124	236	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853185.1	s__UBA953 sp903853185	81.1359	248	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	98.54	98.54	0.77	0.77	2	-
GCA_002293125.1	s__UBA953 sp002293125	81.0749	327	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.83	99.83	0.93	0.93	2	-
GCA_903913915.1	s__UBA953 sp903913915	80.8763	366	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.51	99.16	0.93	0.89	3	-
GCA_016871725.1	s__UBA953 sp016871725	80.7482	326	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917805.1	s__UBA953 sp009917805	80.4734	218	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903921665.1	s__UBA953 sp903921665	80.361	275	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014193315.1	s__UBA953 sp003569405	79.6287	261	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	97.72	96.62	0.94	0.91	4	-
GCA_003569245.1	s__UBA953 sp003569245	79.4177	274	616	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:56:33,896] [INFO] GTDB search result was written to GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/result_gtdb.tsv
[2023-06-30 00:56:33,897] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:56:33,900] [INFO] DFAST_QC result json was written to GCA_903908005.1_freshwater_MAG_---_Umea2_bin-1375_genomic.fna/dqc_result.json
[2023-06-30 00:56:33,900] [INFO] DFAST_QC completed!
[2023-06-30 00:56:33,900] [INFO] Total running time: 0h1m19s