[2023-06-08 20:36:30,317] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:36:30,320] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:36:30,320] [INFO] DQC Reference Directory: /var/lib/cwl/stg6be38c13-63a8-432a-8120-f9adf0e8363e/dqc_reference
[2023-06-08 20:36:31,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:36:31,537] [INFO] Task started: Prodigal
[2023-06-08 20:36:31,537] [INFO] Running command: gunzip -c /var/lib/cwl/stg691d78fe-65d2-4e88-ba86-738ad91f46fc/GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:36:35,117] [INFO] Task succeeded: Prodigal
[2023-06-08 20:36:35,118] [INFO] Task started: HMMsearch
[2023-06-08 20:36:35,118] [INFO] Running command: hmmsearch --tblout GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6be38c13-63a8-432a-8120-f9adf0e8363e/dqc_reference/reference_markers.hmm GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:36:35,358] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:36:35,360] [INFO] Found 6/6 markers.
[2023-06-08 20:36:35,381] [INFO] Query marker FASTA was written to GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 20:36:35,381] [INFO] Task started: Blastn
[2023-06-08 20:36:35,382] [INFO] Running command: blastn -query GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6be38c13-63a8-432a-8120-f9adf0e8363e/dqc_reference/reference_markers.fasta -out GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:36:36,144] [INFO] Task succeeded: Blastn
[2023-06-08 20:36:36,151] [INFO] Selected 30 target genomes.
[2023-06-08 20:36:36,151] [INFO] Target genome list was writen to GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 20:36:36,152] [INFO] Task started: fastANI
[2023-06-08 20:36:36,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg691d78fe-65d2-4e88-ba86-738ad91f46fc/GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:36:51,405] [INFO] Task succeeded: fastANI
[2023-06-08 20:36:51,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6be38c13-63a8-432a-8120-f9adf0e8363e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:36:51,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6be38c13-63a8-432a-8120-f9adf0e8363e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:36:51,408] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:36:51,408] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 20:36:51,408] [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 20:36:51,410] [INFO] DFAST Taxonomy check result was written to GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 20:36:51,411] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:36:51,411] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:36:51,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6be38c13-63a8-432a-8120-f9adf0e8363e/dqc_reference/checkm_data
[2023-06-08 20:36:51,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:36:51,435] [INFO] Task started: CheckM
[2023-06-08 20:36:51,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 20:37:11,024] [INFO] Task succeeded: CheckM
[2023-06-08 20:37:11,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:37:11,052] [INFO] ===== Completeness check finished =====
[2023-06-08 20:37:11,052] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:37:11,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 20:37:11,053] [INFO] Task started: Blastn
[2023-06-08 20:37:11,053] [INFO] Running command: blastn -query GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6be38c13-63a8-432a-8120-f9adf0e8363e/dqc_reference/reference_markers_gtdb.fasta -out GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:37:11,788] [INFO] Task succeeded: Blastn
[2023-06-08 20:37:11,799] [INFO] Selected 21 target genomes.
[2023-06-08 20:37:11,800] [INFO] Target genome list was writen to GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:37:11,802] [INFO] Task started: fastANI
[2023-06-08 20:37:11,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg691d78fe-65d2-4e88-ba86-738ad91f46fc/GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:37:22,574] [INFO] Task succeeded: fastANI
[2023-06-08 20:37:22,587] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:37:22,587] [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_018384375.1	s__CAG-95 sp018384375	99.4962	427	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.73	98.22	0.80	0.77	3	conclusive
GCA_017622575.1	s__CAG-95 sp017622575	78.2604	120	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774465.1	s__CAG-95 sp009774465	77.7908	105	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.09	98.09	0.83	0.83	2	-
GCA_017621815.1	s__CAG-95 sp017621815	77.6074	98	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804785.1	s__CAG-95 sp014804785	77.531	135	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002490775.1	s__CAG-95 sp002490775	77.4814	97	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002492465.1	s__CAG-95 sp002492465	77.3355	101	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017411305.1	s__CAG-95 sp017411305	77.3099	101	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436115.1	s__CAG-95 sp000436115	77.3088	141	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.37	99.32	0.91	0.90	3	-
GCA_009917485.1	s__CAG-95 sp009917485	77.214	106	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803415.1	s__CAG-95 sp014803415	77.1997	97	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	97.80	97.80	0.82	0.82	2	-
GCA_014804285.1	s__CAG-95 sp014804285	77.1293	107	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585005.1	s__CAG-95 sp910585005	76.8547	113	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553305.1	s__CAG-95 sp900553305	76.7665	76	439	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.81	99.81	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-08 20:37:22,590] [INFO] GTDB search result was written to GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 20:37:22,591] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:37:22,596] [INFO] DFAST_QC result json was written to GCA_945831735.1_SRR5976183_bin.13_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 20:37:22,596] [INFO] DFAST_QC completed!
[2023-06-08 20:37:22,596] [INFO] Total running time: 0h0m52s