[2023-06-08 07:54:26,348] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:54:26,352] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:54:26,352] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4c62316-0a5b-48a1-bfd9-0559c126cd64/dqc_reference
[2023-06-08 07:54:27,727] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:54:27,728] [INFO] Task started: Prodigal
[2023-06-08 07:54:27,728] [INFO] Running command: gunzip -c /var/lib/cwl/stg926d8b1f-4898-4e6f-9677-581557f4af20/GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:54:34,175] [INFO] Task succeeded: Prodigal
[2023-06-08 07:54:34,175] [INFO] Task started: HMMsearch
[2023-06-08 07:54:34,175] [INFO] Running command: hmmsearch --tblout GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4c62316-0a5b-48a1-bfd9-0559c126cd64/dqc_reference/reference_markers.hmm GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:54:34,437] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:54:34,439] [INFO] Found 6/6 markers.
[2023-06-08 07:54:34,474] [INFO] Query marker FASTA was written to GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 07:54:34,474] [INFO] Task started: Blastn
[2023-06-08 07:54:34,474] [INFO] Running command: blastn -query GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4c62316-0a5b-48a1-bfd9-0559c126cd64/dqc_reference/reference_markers.fasta -out GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:54:35,162] [INFO] Task succeeded: Blastn
[2023-06-08 07:54:35,166] [INFO] Selected 23 target genomes.
[2023-06-08 07:54:35,166] [INFO] Target genome list was writen to GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 07:54:35,168] [INFO] Task started: fastANI
[2023-06-08 07:54:35,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg926d8b1f-4898-4e6f-9677-581557f4af20/GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:54:47,204] [INFO] Task succeeded: fastANI
[2023-06-08 07:54:47,205] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4c62316-0a5b-48a1-bfd9-0559c126cd64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:54:47,205] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4c62316-0a5b-48a1-bfd9-0559c126cd64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:54:47,211] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:54:47,211] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 07:54:47,211] [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 07:54:47,214] [INFO] DFAST Taxonomy check result was written to GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 07:54:47,215] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:54:47,215] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:54:47,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4c62316-0a5b-48a1-bfd9-0559c126cd64/dqc_reference/checkm_data
[2023-06-08 07:54:47,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:54:47,269] [INFO] Task started: CheckM
[2023-06-08 07:54:47,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 07:55:12,914] [INFO] Task succeeded: CheckM
[2023-06-08 07:55:12,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:55:12,940] [INFO] ===== Completeness check finished =====
[2023-06-08 07:55:12,940] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:55:12,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 07:55:12,941] [INFO] Task started: Blastn
[2023-06-08 07:55:12,941] [INFO] Running command: blastn -query GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4c62316-0a5b-48a1-bfd9-0559c126cd64/dqc_reference/reference_markers_gtdb.fasta -out GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:55:13,930] [INFO] Task succeeded: Blastn
[2023-06-08 07:55:13,950] [INFO] Selected 12 target genomes.
[2023-06-08 07:55:13,951] [INFO] Target genome list was writen to GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:55:13,960] [INFO] Task started: fastANI
[2023-06-08 07:55:13,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg926d8b1f-4898-4e6f-9677-581557f4af20/GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:55:21,666] [INFO] Task succeeded: fastANI
[2023-06-08 07:55:21,680] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:55:21,681] [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_910588335.1	s__Ruminiclostridium_E sp910588335	98.2502	838	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910585505.1	s__Ruminiclostridium_E sp910585505	94.8527	691	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799365.1	s__Ruminiclostridium_E sp014799365	78.9948	336	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	97.60	97.60	0.81	0.81	2	-
GCA_014796735.1	s__Ruminiclostridium_E sp014796735	78.7519	253	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579265.1	s__Ruminiclostridium_E sp910579265	77.5803	192	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799325.1	s__Ruminiclostridium_E sp014799325	77.3235	146	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003508605.1	s__Ruminiclostridium_E sp003508605	77.2767	150	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 07:55:21,683] [INFO] GTDB search result was written to GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 07:55:21,683] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:55:21,687] [INFO] DFAST_QC result json was written to GCA_947574005.1_SRR15730551_bin.34_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 07:55:21,687] [INFO] DFAST_QC completed!
[2023-06-08 07:55:21,687] [INFO] Total running time: 0h0m55s