[2023-06-29 12:18:11,370] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:18:11,372] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:18:11,373] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd6d164a-015b-40c3-a961-bcd4a12e2803/dqc_reference
[2023-06-29 12:18:12,575] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:18:12,576] [INFO] Task started: Prodigal
[2023-06-29 12:18:12,576] [INFO] Running command: gunzip -c /var/lib/cwl/stga7ff81bf-bd46-4eb3-8ec6-7e9f0fa55afd/GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:18:26,861] [INFO] Task succeeded: Prodigal
[2023-06-29 12:18:26,862] [INFO] Task started: HMMsearch
[2023-06-29 12:18:26,862] [INFO] Running command: hmmsearch --tblout GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd6d164a-015b-40c3-a961-bcd4a12e2803/dqc_reference/reference_markers.hmm GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:18:27,097] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:18:27,099] [INFO] Found 6/6 markers.
[2023-06-29 12:18:27,124] [INFO] Query marker FASTA was written to GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 12:18:27,124] [INFO] Task started: Blastn
[2023-06-29 12:18:27,124] [INFO] Running command: blastn -query GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd6d164a-015b-40c3-a961-bcd4a12e2803/dqc_reference/reference_markers.fasta -out GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:18:27,721] [INFO] Task succeeded: Blastn
[2023-06-29 12:18:27,726] [INFO] Selected 22 target genomes.
[2023-06-29 12:18:27,727] [INFO] Target genome list was writen to GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 12:18:27,734] [INFO] Task started: fastANI
[2023-06-29 12:18:27,735] [INFO] Running command: fastANI --query /var/lib/cwl/stga7ff81bf-bd46-4eb3-8ec6-7e9f0fa55afd/GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:18:40,091] [INFO] Task succeeded: fastANI
[2023-06-29 12:18:40,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd6d164a-015b-40c3-a961-bcd4a12e2803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:18:40,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd6d164a-015b-40c3-a961-bcd4a12e2803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:18:40,098] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:18:40,098] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:18:40,098] [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
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	77.6646	168	788	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:18:40,100] [INFO] DFAST Taxonomy check result was written to GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 12:18:40,101] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:18:40,101] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:18:40,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd6d164a-015b-40c3-a961-bcd4a12e2803/dqc_reference/checkm_data
[2023-06-29 12:18:40,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:18:40,132] [INFO] Task started: CheckM
[2023-06-29 12:18:40,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 12:19:22,935] [INFO] Task succeeded: CheckM
[2023-06-29 12:19:22,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 12:19:22,956] [INFO] ===== Completeness check finished =====
[2023-06-29 12:19:22,957] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:19:22,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 12:19:22,957] [INFO] Task started: Blastn
[2023-06-29 12:19:22,957] [INFO] Running command: blastn -query GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd6d164a-015b-40c3-a961-bcd4a12e2803/dqc_reference/reference_markers_gtdb.fasta -out GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:19:23,791] [INFO] Task succeeded: Blastn
[2023-06-29 12:19:23,795] [INFO] Selected 15 target genomes.
[2023-06-29 12:19:23,795] [INFO] Target genome list was writen to GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:19:23,806] [INFO] Task started: fastANI
[2023-06-29 12:19:23,806] [INFO] Running command: fastANI --query /var/lib/cwl/stga7ff81bf-bd46-4eb3-8ec6-7e9f0fa55afd/GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:19:31,123] [INFO] Task succeeded: fastANI
[2023-06-29 12:19:31,140] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:19:31,140] [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_905210875.1	s__UBA11471 sp905210875	98.6365	556	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900542765.1	s__UBA11471 sp900542765	84.5023	558	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	98.30	98.30	0.95	0.95	2	-
GCA_900547555.1	s__UBA11471 sp900547555	79.5014	358	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	98.22	98.22	0.90	0.90	2	-
GCA_000434215.1	s__UBA11471 sp000434215	79.2026	370	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	99.32	98.64	0.92	0.84	6	-
GCA_017462265.1	s__UBA11471 sp017462265	78.2735	203	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115485.1	s__Barnesiella excrementavium	77.7229	154	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512915.1	s__Barnesiella viscericola	77.6619	169	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	97.37	97.37	0.91	0.91	2	-
GCF_002159975.1	s__Barnesiella merdigallinarum	77.6215	157	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	97.77	95.24	0.93	0.91	5	-
GCA_018714665.1	s__Gallibacteroides avistercoris	76.9181	61	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__CHK158-818;g__Gallibacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116805.1	s__Bacteroides merdavium	76.0103	61	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:19:31,142] [INFO] GTDB search result was written to GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 12:19:31,143] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:19:31,148] [INFO] DFAST_QC result json was written to GCA_937992045.1_ERR911998_bin.137_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 12:19:31,148] [INFO] DFAST_QC completed!
[2023-06-29 12:19:31,148] [INFO] Total running time: 0h1m20s