[2023-06-29 13:18:59,400] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:18:59,403] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:18:59,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg243896ce-5f52-4113-ac1a-a8d57ed46806/dqc_reference
[2023-06-29 13:19:00,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:19:00,762] [INFO] Task started: Prodigal
[2023-06-29 13:19:00,762] [INFO] Running command: gunzip -c /var/lib/cwl/stgb557652e-902f-4ce5-bd1d-f75940e166cf/GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:19:04,632] [INFO] Task succeeded: Prodigal
[2023-06-29 13:19:04,633] [INFO] Task started: HMMsearch
[2023-06-29 13:19:04,633] [INFO] Running command: hmmsearch --tblout GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg243896ce-5f52-4113-ac1a-a8d57ed46806/dqc_reference/reference_markers.hmm GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:19:04,860] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:19:04,861] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb557652e-902f-4ce5-bd1d-f75940e166cf/GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 13:19:04,887] [INFO] Query marker FASTA was written to GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 13:19:04,888] [INFO] Task started: Blastn
[2023-06-29 13:19:04,888] [INFO] Running command: blastn -query GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg243896ce-5f52-4113-ac1a-a8d57ed46806/dqc_reference/reference_markers.fasta -out GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:19:05,591] [INFO] Task succeeded: Blastn
[2023-06-29 13:19:05,595] [INFO] Selected 17 target genomes.
[2023-06-29 13:19:05,595] [INFO] Target genome list was writen to GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 13:19:05,597] [INFO] Task started: fastANI
[2023-06-29 13:19:05,598] [INFO] Running command: fastANI --query /var/lib/cwl/stgb557652e-902f-4ce5-bd1d-f75940e166cf/GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:19:13,444] [INFO] Task succeeded: fastANI
[2023-06-29 13:19:13,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg243896ce-5f52-4113-ac1a-a8d57ed46806/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:19:13,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg243896ce-5f52-4113-ac1a-a8d57ed46806/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:19:13,447] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:19:13,448] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 13:19:13,448] [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 13:19:13,450] [INFO] DFAST Taxonomy check result was written to GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 13:19:13,451] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:19:13,451] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:19:13,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg243896ce-5f52-4113-ac1a-a8d57ed46806/dqc_reference/checkm_data
[2023-06-29 13:19:13,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:19:13,476] [INFO] Task started: CheckM
[2023-06-29 13:19:13,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 13:19:33,168] [INFO] Task succeeded: CheckM
[2023-06-29 13:19:33,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.93%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:19:33,194] [INFO] ===== Completeness check finished =====
[2023-06-29 13:19:33,194] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:19:33,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 13:19:33,195] [INFO] Task started: Blastn
[2023-06-29 13:19:33,195] [INFO] Running command: blastn -query GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg243896ce-5f52-4113-ac1a-a8d57ed46806/dqc_reference/reference_markers_gtdb.fasta -out GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:19:34,326] [INFO] Task succeeded: Blastn
[2023-06-29 13:19:34,333] [INFO] Selected 10 target genomes.
[2023-06-29 13:19:34,333] [INFO] Target genome list was writen to GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:19:34,341] [INFO] Task started: fastANI
[2023-06-29 13:19:34,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgb557652e-902f-4ce5-bd1d-f75940e166cf/GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:19:37,784] [INFO] Task succeeded: fastANI
[2023-06-29 13:19:37,790] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:19:37,790] [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_900552845.1	s__Angelakisella sp900552845	99.0985	289	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	98.71	98.15	0.74	0.74	3	conclusive
GCA_900547385.1	s__Angelakisella sp900547385	83.9794	254	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	97.71	97.52	0.88	0.82	7	-
GCA_004557855.1	s__Angelakisella sp004557855	83.8183	253	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	98.10	97.70	0.90	0.86	7	-
GCA_003453215.1	s__Angelakisella sp003453215	81.8602	195	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004554485.1	s__Angelakisella sp004554485	81.3945	195	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	97.18	96.00	0.84	0.76	6	-
--------------------------------------------------------------------------------
[2023-06-29 13:19:37,793] [INFO] GTDB search result was written to GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 13:19:37,793] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:19:37,796] [INFO] DFAST_QC result json was written to GCA_937981925.1_SRR5580040_bin.19_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 13:19:37,796] [INFO] DFAST_QC completed!
[2023-06-29 13:19:37,796] [INFO] Total running time: 0h0m38s