[2023-06-29 20:35:14,276] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:35:14,285] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:35:14,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg098f2c1f-326a-47f3-9ea2-b6f110e005b1/dqc_reference
[2023-06-29 20:35:15,567] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:35:15,568] [INFO] Task started: Prodigal
[2023-06-29 20:35:15,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg934560ef-fb85-4aeb-aef6-ea335ca9c1eb/GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:35:27,670] [INFO] Task succeeded: Prodigal
[2023-06-29 20:35:27,670] [INFO] Task started: HMMsearch
[2023-06-29 20:35:27,670] [INFO] Running command: hmmsearch --tblout GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg098f2c1f-326a-47f3-9ea2-b6f110e005b1/dqc_reference/reference_markers.hmm GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:35:27,974] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:35:27,978] [INFO] Found 6/6 markers.
[2023-06-29 20:35:28,012] [INFO] Query marker FASTA was written to GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 20:35:28,012] [INFO] Task started: Blastn
[2023-06-29 20:35:28,012] [INFO] Running command: blastn -query GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg098f2c1f-326a-47f3-9ea2-b6f110e005b1/dqc_reference/reference_markers.fasta -out GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:35:28,624] [INFO] Task succeeded: Blastn
[2023-06-29 20:35:28,629] [INFO] Selected 25 target genomes.
[2023-06-29 20:35:28,630] [INFO] Target genome list was writen to GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 20:35:28,634] [INFO] Task started: fastANI
[2023-06-29 20:35:28,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg934560ef-fb85-4aeb-aef6-ea335ca9c1eb/GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:35:42,180] [INFO] Task succeeded: fastANI
[2023-06-29 20:35:42,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg098f2c1f-326a-47f3-9ea2-b6f110e005b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:35:42,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg098f2c1f-326a-47f3-9ea2-b6f110e005b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:35:42,183] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:35:42,184] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 20:35:42,184] [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
--------------------------------------------------------------------------------
[2023-06-29 20:35:42,187] [INFO] DFAST Taxonomy check result was written to GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 20:35:42,187] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:35:42,188] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:35:42,188] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg098f2c1f-326a-47f3-9ea2-b6f110e005b1/dqc_reference/checkm_data
[2023-06-29 20:35:42,193] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:35:42,218] [INFO] Task started: CheckM
[2023-06-29 20:35:42,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 20:36:19,694] [INFO] Task succeeded: CheckM
[2023-06-29 20:36:19,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:36:19,730] [INFO] ===== Completeness check finished =====
[2023-06-29 20:36:19,730] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:36:19,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 20:36:19,731] [INFO] Task started: Blastn
[2023-06-29 20:36:19,731] [INFO] Running command: blastn -query GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg098f2c1f-326a-47f3-9ea2-b6f110e005b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:36:20,601] [INFO] Task succeeded: Blastn
[2023-06-29 20:36:20,607] [INFO] Selected 17 target genomes.
[2023-06-29 20:36:20,607] [INFO] Target genome list was writen to GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:36:20,627] [INFO] Task started: fastANI
[2023-06-29 20:36:20,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg934560ef-fb85-4aeb-aef6-ea335ca9c1eb/GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:36:28,243] [INFO] Task succeeded: fastANI
[2023-06-29 20:36:28,267] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:36:28,267] [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_017634595.1	s__Cryptobacteroides sp017634595	80.7268	375	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792815.1	s__Cryptobacteroides sp902792815	79.9755	326	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.52	96.82	0.86	0.75	13	-
GCA_017651465.1	s__Cryptobacteroides sp017651465	79.6303	287	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782225.1	s__Cryptobacteroides sp902782225	79.4143	296	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.55	97.13	0.87	0.83	3	-
GCA_900318565.1	s__Cryptobacteroides sp900318565	79.295	258	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.62	96.86	0.83	0.73	9	-
GCA_017561765.1	s__Cryptobacteroides sp017561765	79.2385	262	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766255.1	s__Cryptobacteroides sp902766255	78.6339	259	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017554335.1	s__Cryptobacteroides sp017554335	78.5225	220	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016288775.1	s__Cryptobacteroides sp016288775	78.3368	236	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780175.1	s__Cryptobacteroides sp902780175	78.2865	179	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	95.78	95.78	0.73	0.73	2	-
GCA_017617715.1	s__Cryptobacteroides sp017617715	78.2645	243	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017454265.1	s__Cryptobacteroides sp017454265	78.0506	174	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017615615.1	s__Cryptobacteroides sp017615615	77.9973	131	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:36:28,270] [INFO] GTDB search result was written to GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 20:36:28,270] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:36:28,273] [INFO] DFAST_QC result json was written to GCA_946613165.1_SRR873608_bin.85_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 20:36:28,273] [INFO] DFAST_QC completed!
[2023-06-29 20:36:28,274] [INFO] Total running time: 0h1m14s