[2023-06-29 14:46:17,494] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:46:17,496] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:46:17,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg071d7654-795d-4845-96a6-30d2c623cae5/dqc_reference
[2023-06-29 14:46:18,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:46:18,852] [INFO] Task started: Prodigal
[2023-06-29 14:46:18,852] [INFO] Running command: gunzip -c /var/lib/cwl/stg3861b55d-a610-412e-8153-73603579fda9/GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:46:23,792] [INFO] Task succeeded: Prodigal
[2023-06-29 14:46:23,792] [INFO] Task started: HMMsearch
[2023-06-29 14:46:23,792] [INFO] Running command: hmmsearch --tblout GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg071d7654-795d-4845-96a6-30d2c623cae5/dqc_reference/reference_markers.hmm GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:46:24,047] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:46:24,049] [INFO] Found 6/6 markers.
[2023-06-29 14:46:24,070] [INFO] Query marker FASTA was written to GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 14:46:24,070] [INFO] Task started: Blastn
[2023-06-29 14:46:24,071] [INFO] Running command: blastn -query GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg071d7654-795d-4845-96a6-30d2c623cae5/dqc_reference/reference_markers.fasta -out GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:46:24,728] [INFO] Task succeeded: Blastn
[2023-06-29 14:46:24,736] [INFO] Selected 31 target genomes.
[2023-06-29 14:46:24,737] [INFO] Target genome list was writen to GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 14:46:24,739] [INFO] Task started: fastANI
[2023-06-29 14:46:24,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg3861b55d-a610-412e-8153-73603579fda9/GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:46:44,077] [INFO] Task succeeded: fastANI
[2023-06-29 14:46:44,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg071d7654-795d-4845-96a6-30d2c623cae5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:46:44,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg071d7654-795d-4845-96a6-30d2c623cae5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:46:44,080] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:46:44,080] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 14:46:44,080] [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 14:46:44,083] [INFO] DFAST Taxonomy check result was written to GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 14:46:44,083] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:46:44,084] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:46:44,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg071d7654-795d-4845-96a6-30d2c623cae5/dqc_reference/checkm_data
[2023-06-29 14:46:44,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:46:44,117] [INFO] Task started: CheckM
[2023-06-29 14:46:44,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 14:47:06,499] [INFO] Task succeeded: CheckM
[2023-06-29 14:47:06,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 3.12%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-29 14:47:06,529] [INFO] ===== Completeness check finished =====
[2023-06-29 14:47:06,529] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:47:06,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 14:47:06,530] [INFO] Task started: Blastn
[2023-06-29 14:47:06,530] [INFO] Running command: blastn -query GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg071d7654-795d-4845-96a6-30d2c623cae5/dqc_reference/reference_markers_gtdb.fasta -out GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:47:07,628] [INFO] Task succeeded: Blastn
[2023-06-29 14:47:07,632] [INFO] Selected 11 target genomes.
[2023-06-29 14:47:07,633] [INFO] Target genome list was writen to GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:47:07,637] [INFO] Task started: fastANI
[2023-06-29 14:47:07,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg3861b55d-a610-412e-8153-73603579fda9/GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:47:12,780] [INFO] Task succeeded: fastANI
[2023-06-29 14:47:12,792] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:47:12,792] [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_004554245.1	s__Oribacterium sp004554245	96.1911	533	593	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	95.82	95.50	0.87	0.83	4	conclusive
GCA_900770445.1	s__Oribacterium sp900770445	93.8182	508	593	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900772695.1	s__Oribacterium sp900772695	92.3504	391	593	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002431355.1	s__Oribacterium sp002431355	81.6293	374	593	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	99.25	99.25	0.80	0.80	2	-
GCF_002007235.1	s__Oribacterium sp002007235	78.3944	103	593	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000513555.1	s__Oribacterium sp000513555	78.2128	114	593	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315665.1	s__Oribacterium sp900315665	77.9711	150	593	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	99.12	99.08	0.89	0.88	3	-
GCF_013394775.1	s__Oribacterium sp013394775	77.1409	100	593	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:47:12,794] [INFO] GTDB search result was written to GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 14:47:12,795] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:47:12,798] [INFO] DFAST_QC result json was written to GCA_937968645.1_SRR3993004_bin.83_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 14:47:12,798] [INFO] DFAST_QC completed!
[2023-06-29 14:47:12,798] [INFO] Total running time: 0h0m55s