[2023-06-29 22:41:15,246] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:41:15,264] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:41:15,264] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf133dee-f9b5-4d41-a6d8-59fa5555106d/dqc_reference
[2023-06-29 22:41:16,589] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:41:16,590] [INFO] Task started: Prodigal
[2023-06-29 22:41:16,591] [INFO] Running command: gunzip -c /var/lib/cwl/stg78816fb7-c303-4a60-a31c-5d53398d3b39/GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna.gz | prodigal -d GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/cds.fna -a GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:41:23,261] [INFO] Task succeeded: Prodigal
[2023-06-29 22:41:23,261] [INFO] Task started: HMMsearch
[2023-06-29 22:41:23,261] [INFO] Running command: hmmsearch --tblout GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf133dee-f9b5-4d41-a6d8-59fa5555106d/dqc_reference/reference_markers.hmm GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:41:23,479] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:41:23,481] [INFO] Found 6/6 markers.
[2023-06-29 22:41:23,497] [INFO] Query marker FASTA was written to GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/markers.fasta
[2023-06-29 22:41:23,498] [INFO] Task started: Blastn
[2023-06-29 22:41:23,498] [INFO] Running command: blastn -query GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf133dee-f9b5-4d41-a6d8-59fa5555106d/dqc_reference/reference_markers.fasta -out GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:41:24,093] [INFO] Task succeeded: Blastn
[2023-06-29 22:41:24,098] [INFO] Selected 15 target genomes.
[2023-06-29 22:41:24,098] [INFO] Target genome list was writen to GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/target_genomes.txt
[2023-06-29 22:41:24,100] [INFO] Task started: fastANI
[2023-06-29 22:41:24,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg78816fb7-c303-4a60-a31c-5d53398d3b39/GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna.gz --refList GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/target_genomes.txt --output GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:41:31,869] [INFO] Task succeeded: fastANI
[2023-06-29 22:41:31,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf133dee-f9b5-4d41-a6d8-59fa5555106d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:41:31,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf133dee-f9b5-4d41-a6d8-59fa5555106d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:41:31,872] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:41:31,872] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 22:41:31,872] [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 22:41:31,874] [INFO] DFAST Taxonomy check result was written to GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/tc_result.tsv
[2023-06-29 22:41:31,874] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:41:31,875] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:41:31,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf133dee-f9b5-4d41-a6d8-59fa5555106d/dqc_reference/checkm_data
[2023-06-29 22:41:31,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:41:31,896] [INFO] Task started: CheckM
[2023-06-29 22:41:31,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/checkm_input GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/checkm_result
[2023-06-29 22:41:58,674] [INFO] Task succeeded: CheckM
[2023-06-29 22:41:58,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:41:58,695] [INFO] ===== Completeness check finished =====
[2023-06-29 22:41:58,695] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:41:58,696] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/markers.fasta)
[2023-06-29 22:41:58,696] [INFO] Task started: Blastn
[2023-06-29 22:41:58,696] [INFO] Running command: blastn -query GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf133dee-f9b5-4d41-a6d8-59fa5555106d/dqc_reference/reference_markers_gtdb.fasta -out GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:41:59,538] [INFO] Task succeeded: Blastn
[2023-06-29 22:41:59,542] [INFO] Selected 9 target genomes.
[2023-06-29 22:41:59,543] [INFO] Target genome list was writen to GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:41:59,545] [INFO] Task started: fastANI
[2023-06-29 22:41:59,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg78816fb7-c303-4a60-a31c-5d53398d3b39/GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna.gz --refList GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/target_genomes_gtdb.txt --output GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:42:02,013] [INFO] Task succeeded: fastANI
[2023-06-29 22:42:02,028] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:42:02,028] [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_903861715.1	s__CAIPMZ01 sp903861715	99.9451	341	351	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__GWC2-37-73;g__CAIPMZ01	95.0	97.86	95.05	0.89	0.78	25	conclusive
GCA_903851135.1	s__CAIPMZ01 sp903851135	83.2788	208	351	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__GWC2-37-73;g__CAIPMZ01	95.0	99.97	99.95	0.99	0.98	6	-
GCA_903885965.1	s__CAIPMZ01 sp903885965	81.9747	159	351	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__GWC2-37-73;g__CAIPMZ01	95.0	100.00	100.00	0.98	0.98	3	-
GCA_903824515.1	s__CAIPMZ01 sp903824515	80.8801	165	351	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__GWC2-37-73;g__CAIPMZ01	95.0	99.60	99.29	0.91	0.89	3	-
GCA_903837175.1	s__CAIPMZ01 sp903837175	80.0169	139	351	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__GWC2-37-73;g__CAIPMZ01	95.0	99.87	99.87	0.92	0.92	2	-
GCA_903866285.1	s__CAIPMZ01 sp903866285	79.9851	128	351	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__GWC2-37-73;g__CAIPMZ01	95.0	99.85	99.84	0.93	0.93	3	-
GCA_013336225.1	s__UBA12068 sp013336225	77.6285	68	351	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__GWC2-37-73;g__UBA12068	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 22:42:02,030] [INFO] GTDB search result was written to GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/result_gtdb.tsv
[2023-06-29 22:42:02,031] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:42:02,035] [INFO] DFAST_QC result json was written to GCA_903855795.1_freshwater_MAG_---_MJ110629B_bin-623_genomic.fna/dqc_result.json
[2023-06-29 22:42:02,035] [INFO] DFAST_QC completed!
[2023-06-29 22:42:02,036] [INFO] Total running time: 0h0m47s