[2023-06-30 10:36:31,924] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:36:31,929] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:36:31,929] [INFO] DQC Reference Directory: /var/lib/cwl/stge567d5ba-5baa-47c7-b5c6-24e84509feb6/dqc_reference
[2023-06-30 10:36:33,156] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:36:33,157] [INFO] Task started: Prodigal
[2023-06-30 10:36:33,158] [INFO] Running command: gunzip -c /var/lib/cwl/stg37615987-b615-48d6-ab5e-a48fac8a575b/GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:36:42,267] [INFO] Task succeeded: Prodigal
[2023-06-30 10:36:42,267] [INFO] Task started: HMMsearch
[2023-06-30 10:36:42,267] [INFO] Running command: hmmsearch --tblout GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge567d5ba-5baa-47c7-b5c6-24e84509feb6/dqc_reference/reference_markers.hmm GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:36:42,500] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:36:42,502] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg37615987-b615-48d6-ab5e-a48fac8a575b/GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-30 10:36:42,525] [INFO] Query marker FASTA was written to GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-30 10:36:42,525] [INFO] Task started: Blastn
[2023-06-30 10:36:42,525] [INFO] Running command: blastn -query GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stge567d5ba-5baa-47c7-b5c6-24e84509feb6/dqc_reference/reference_markers.fasta -out GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:36:43,077] [INFO] Task succeeded: Blastn
[2023-06-30 10:36:43,081] [INFO] Selected 14 target genomes.
[2023-06-30 10:36:43,082] [INFO] Target genome list was writen to GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-30 10:36:43,083] [INFO] Task started: fastANI
[2023-06-30 10:36:43,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg37615987-b615-48d6-ab5e-a48fac8a575b/GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:36:53,439] [INFO] Task succeeded: fastANI
[2023-06-30 10:36:53,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge567d5ba-5baa-47c7-b5c6-24e84509feb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:36:53,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge567d5ba-5baa-47c7-b5c6-24e84509feb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:36:53,442] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:36:53,442] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 10:36:53,442] [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 10:36:53,444] [INFO] DFAST Taxonomy check result was written to GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-30 10:36:53,445] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:36:53,445] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:36:53,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge567d5ba-5baa-47c7-b5c6-24e84509feb6/dqc_reference/checkm_data
[2023-06-30 10:36:53,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:36:53,468] [INFO] Task started: CheckM
[2023-06-30 10:36:53,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-30 10:37:25,178] [INFO] Task succeeded: CheckM
[2023-06-30 10:37:25,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 10:37:25,200] [INFO] ===== Completeness check finished =====
[2023-06-30 10:37:25,201] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:37:25,201] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-30 10:37:25,201] [INFO] Task started: Blastn
[2023-06-30 10:37:25,202] [INFO] Running command: blastn -query GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stge567d5ba-5baa-47c7-b5c6-24e84509feb6/dqc_reference/reference_markers_gtdb.fasta -out GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:37:25,763] [INFO] Task succeeded: Blastn
[2023-06-30 10:37:25,767] [INFO] Selected 14 target genomes.
[2023-06-30 10:37:25,767] [INFO] Target genome list was writen to GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:37:25,770] [INFO] Task started: fastANI
[2023-06-30 10:37:25,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg37615987-b615-48d6-ab5e-a48fac8a575b/GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:37:31,714] [INFO] Task succeeded: fastANI
[2023-06-30 10:37:31,734] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:37:31,734] [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_002369075.1	s__RF16 sp002369075	99.5272	393	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905233255.1	s__RF16 sp905233255	87.4309	370	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799185.1	s__RF16 sp902799185	81.9764	265	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774995.1	s__RF16 sp902774995	81.5091	258	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	95.68	95.65	0.72	0.66	3	-
GCA_002373505.1	s__RF16 sp002373505	81.1221	254	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.32	96.25	0.84	0.83	3	-
GCA_900316845.1	s__RF16 sp900316845	80.6007	254	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.47	95.23	0.82	0.74	5	-
GCA_002394395.1	s__RF16 sp002394395	80.5161	237	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792535.1	s__RF16 sp902792535	80.4156	242	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765485.1	s__RF16 sp902765485	80.2333	210	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.12	96.12	0.76	0.76	2	-
GCA_900317885.1	s__RF16 sp900317885	80.0537	247	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.25	96.25	0.86	0.83	5	-
GCA_902778935.1	s__RF16 sp902778935	79.295	203	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.50	96.20	0.85	0.83	6	-
GCA_900319005.1	s__RF16 sp900319005	79.2635	184	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.76	96.71	0.85	0.80	4	-
GCA_900319645.1	s__RF16 sp900319645	78.9582	199	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.68	95.36	0.92	0.85	3	-
GCA_902799555.1	s__RF16 sp902799555	78.2448	178	500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.18	96.01	0.81	0.78	3	-
--------------------------------------------------------------------------------
[2023-06-30 10:37:31,736] [INFO] GTDB search result was written to GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 10:37:31,737] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:37:31,740] [INFO] DFAST_QC result json was written to GCA_946620045.1_SRR873609_bin.134_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-30 10:37:31,741] [INFO] DFAST_QC completed!
[2023-06-30 10:37:31,741] [INFO] Total running time: 0h0m60s