[2023-06-28 14:05:58,617] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:05:58,619] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:05:58,620] [INFO] DQC Reference Directory: /var/lib/cwl/stgf54259b4-d2c2-4f82-ae29-e62ac3453221/dqc_reference
[2023-06-28 14:05:59,843] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:05:59,844] [INFO] Task started: Prodigal
[2023-06-28 14:05:59,844] [INFO] Running command: gunzip -c /var/lib/cwl/stg06fdadba-d4fd-4d85-a8de-d141bd904514/GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:06:03,111] [INFO] Task succeeded: Prodigal
[2023-06-28 14:06:03,112] [INFO] Task started: HMMsearch
[2023-06-28 14:06:03,112] [INFO] Running command: hmmsearch --tblout GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf54259b4-d2c2-4f82-ae29-e62ac3453221/dqc_reference/reference_markers.hmm GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:06:03,347] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:06:03,348] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg06fdadba-d4fd-4d85-a8de-d141bd904514/GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-28 14:06:03,371] [INFO] Query marker FASTA was written to GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-28 14:06:03,371] [INFO] Task started: Blastn
[2023-06-28 14:06:03,371] [INFO] Running command: blastn -query GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf54259b4-d2c2-4f82-ae29-e62ac3453221/dqc_reference/reference_markers.fasta -out GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:06:03,954] [INFO] Task succeeded: Blastn
[2023-06-28 14:06:03,974] [INFO] Selected 21 target genomes.
[2023-06-28 14:06:03,974] [INFO] Target genome list was writen to GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-28 14:06:03,982] [INFO] Task started: fastANI
[2023-06-28 14:06:03,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg06fdadba-d4fd-4d85-a8de-d141bd904514/GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:06:16,830] [INFO] Task succeeded: fastANI
[2023-06-28 14:06:16,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf54259b4-d2c2-4f82-ae29-e62ac3453221/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:06:16,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf54259b4-d2c2-4f82-ae29-e62ac3453221/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:06:16,839] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:06:16,840] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 14:06:16,840] [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
[Clostridium] innocuum	strain=ATCC 14501	GCA_018458805.1	1522	1522	type	True	76.3577	52	451	95	below_threshold
[Clostridium] innocuum	strain=ATCC 14501	GCA_012317185.1	1522	1522	type	True	76.3205	50	451	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 14:06:16,842] [INFO] DFAST Taxonomy check result was written to GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-28 14:06:16,843] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:06:16,843] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:06:16,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf54259b4-d2c2-4f82-ae29-e62ac3453221/dqc_reference/checkm_data
[2023-06-28 14:06:16,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:06:16,867] [INFO] Task started: CheckM
[2023-06-28 14:06:16,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-28 14:06:35,459] [INFO] Task succeeded: CheckM
[2023-06-28 14:06:35,460] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:06:35,481] [INFO] ===== Completeness check finished =====
[2023-06-28 14:06:35,482] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:06:35,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-28 14:06:35,482] [INFO] Task started: Blastn
[2023-06-28 14:06:35,483] [INFO] Running command: blastn -query GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf54259b4-d2c2-4f82-ae29-e62ac3453221/dqc_reference/reference_markers_gtdb.fasta -out GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:06:36,310] [INFO] Task succeeded: Blastn
[2023-06-28 14:06:36,314] [INFO] Selected 17 target genomes.
[2023-06-28 14:06:36,314] [INFO] Target genome list was writen to GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:06:36,352] [INFO] Task started: fastANI
[2023-06-28 14:06:36,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg06fdadba-d4fd-4d85-a8de-d141bd904514/GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:06:44,040] [INFO] Task succeeded: fastANI
[2023-06-28 14:06:44,050] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 14:06:44,050] [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_910576855.1	s__C-19 sp910576855	98.6219	438	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__C-19	95.0	99.07	99.07	0.95	0.95	2	conclusive
GCA_009917405.1	s__C-19 sp009917405	83.443	300	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__C-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576345.1	s__C-19 sp910576345	79.4639	70	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__C-19	95.0	99.11	99.11	0.92	0.92	2	-
GCA_910586285.1	s__C-19 sp910586285	77.4931	93	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__C-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017161075.1	s__Clostridium_AQ sp000165065	76.5632	55	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	97.84	97.80	0.84	0.80	7	-
GCF_012317185.1	s__Clostridium_AQ innocuum	76.2831	51	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	97.93	97.20	0.87	0.81	50	-
--------------------------------------------------------------------------------
[2023-06-28 14:06:44,052] [INFO] GTDB search result was written to GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 14:06:44,053] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:06:44,056] [INFO] DFAST_QC result json was written to GCA_948441925.1_SRR17684635_bin.44_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-28 14:06:44,056] [INFO] DFAST_QC completed!
[2023-06-28 14:06:44,057] [INFO] Total running time: 0h0m45s