[2023-06-08 14:53:58,641] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:53:58,644] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:53:58,644] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f7c5533-b949-407c-a2a8-19b12adb2ced/dqc_reference
[2023-06-08 14:54:00,746] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:54:00,747] [INFO] Task started: Prodigal
[2023-06-08 14:54:00,747] [INFO] Running command: gunzip -c /var/lib/cwl/stgae16ff3f-cef0-4029-9453-b803c033d688/GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:54:02,433] [INFO] Task succeeded: Prodigal
[2023-06-08 14:54:02,434] [INFO] Task started: HMMsearch
[2023-06-08 14:54:02,434] [INFO] Running command: hmmsearch --tblout GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f7c5533-b949-407c-a2a8-19b12adb2ced/dqc_reference/reference_markers.hmm GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:54:02,656] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:54:02,658] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgae16ff3f-cef0-4029-9453-b803c033d688/GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 14:54:02,681] [INFO] Query marker FASTA was written to GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 14:54:02,682] [INFO] Task started: Blastn
[2023-06-08 14:54:02,682] [INFO] Running command: blastn -query GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f7c5533-b949-407c-a2a8-19b12adb2ced/dqc_reference/reference_markers.fasta -out GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:54:05,170] [INFO] Task succeeded: Blastn
[2023-06-08 14:54:05,173] [INFO] Selected 26 target genomes.
[2023-06-08 14:54:05,174] [INFO] Target genome list was writen to GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 14:54:05,183] [INFO] Task started: fastANI
[2023-06-08 14:54:05,184] [INFO] Running command: fastANI --query /var/lib/cwl/stgae16ff3f-cef0-4029-9453-b803c033d688/GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:54:15,456] [INFO] Task succeeded: fastANI
[2023-06-08 14:54:15,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f7c5533-b949-407c-a2a8-19b12adb2ced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:54:15,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f7c5533-b949-407c-a2a8-19b12adb2ced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:54:15,459] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:54:15,459] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 14:54:15,459] [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
--------------------------------------------------------------------------------
[2023-06-08 14:54:15,462] [INFO] DFAST Taxonomy check result was written to GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 14:54:15,463] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:54:15,463] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:54:15,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f7c5533-b949-407c-a2a8-19b12adb2ced/dqc_reference/checkm_data
[2023-06-08 14:54:15,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:54:15,486] [INFO] Task started: CheckM
[2023-06-08 14:54:15,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 14:54:29,014] [INFO] Task succeeded: CheckM
[2023-06-08 14:54:29,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:54:29,033] [INFO] ===== Completeness check finished =====
[2023-06-08 14:54:29,033] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:54:29,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 14:54:29,034] [INFO] Task started: Blastn
[2023-06-08 14:54:29,034] [INFO] Running command: blastn -query GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f7c5533-b949-407c-a2a8-19b12adb2ced/dqc_reference/reference_markers_gtdb.fasta -out GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:54:29,846] [INFO] Task succeeded: Blastn
[2023-06-08 14:54:29,851] [INFO] Selected 26 target genomes.
[2023-06-08 14:54:29,851] [INFO] Target genome list was writen to GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:54:29,854] [INFO] Task started: fastANI
[2023-06-08 14:54:29,854] [INFO] Running command: fastANI --query /var/lib/cwl/stgae16ff3f-cef0-4029-9453-b803c033d688/GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:54:35,510] [INFO] Task succeeded: fastANI
[2023-06-08 14:54:35,527] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 14:54:35,527] [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_000436255.1	s__CAG-1193 sp000436255	78.8567	139	369	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1193	95.0	98.61	98.61	0.83	0.83	2	-
GCA_900550145.1	s__CAG-1193 sp900550145	78.6054	121	369	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1193	95.0	98.80	98.48	0.76	0.71	3	-
GCA_017428495.1	s__CAG-1193 sp017428495	78.6016	133	369	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1193	95.0	98.47	98.35	0.88	0.84	3	-
GCA_902783915.1	s__CAG-1193 sp902783915	78.3288	112	369	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1193	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793375.1	s__RUG13868 sp902793375	76.3335	51	369	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG13868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425325.1	s__UBA5578 sp002425325	76.3162	53	369	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017404385.1	s__RUG13038 sp017404385	76.2843	51	369	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG13038	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789225.1	s__RUG343 sp902789225	76.2782	52	369	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG343	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905211265.1	s__HGM10818 sp905211265	76.2566	59	369	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__HGM10818	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434175.1	s__CAG-611 sp000434175	75.7204	63	369	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-611	95.0	98.26	98.26	0.87	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-08 14:54:35,530] [INFO] GTDB search result was written to GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 14:54:35,530] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:54:35,534] [INFO] DFAST_QC result json was written to GCA_945878985.1_SRR17382097_bin.55_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 14:54:35,535] [INFO] DFAST_QC completed!
[2023-06-08 14:54:35,535] [INFO] Total running time: 0h0m37s