[2023-06-08 09:17:51,328] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:17:51,332] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:17:51,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg79cea13d-6198-45fd-97f5-9e4f9eeb464b/dqc_reference
[2023-06-08 09:17:53,181] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:17:53,182] [INFO] Task started: Prodigal
[2023-06-08 09:17:53,183] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb2a1b94-57dc-4c9d-b737-8018f35b85fc/GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:17:56,450] [INFO] Task succeeded: Prodigal
[2023-06-08 09:17:56,450] [INFO] Task started: HMMsearch
[2023-06-08 09:17:56,450] [INFO] Running command: hmmsearch --tblout GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79cea13d-6198-45fd-97f5-9e4f9eeb464b/dqc_reference/reference_markers.hmm GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:17:56,611] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:17:56,612] [INFO] Found 6/6 markers.
[2023-06-08 09:17:56,628] [INFO] Query marker FASTA was written to GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 09:17:56,629] [INFO] Task started: Blastn
[2023-06-08 09:17:56,629] [INFO] Running command: blastn -query GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg79cea13d-6198-45fd-97f5-9e4f9eeb464b/dqc_reference/reference_markers.fasta -out GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:17:57,225] [INFO] Task succeeded: Blastn
[2023-06-08 09:17:57,229] [INFO] Selected 17 target genomes.
[2023-06-08 09:17:57,229] [INFO] Target genome list was writen to GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 09:17:57,230] [INFO] Task started: fastANI
[2023-06-08 09:17:57,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb2a1b94-57dc-4c9d-b737-8018f35b85fc/GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:18:03,944] [INFO] Task succeeded: fastANI
[2023-06-08 09:18:03,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79cea13d-6198-45fd-97f5-9e4f9eeb464b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:18:03,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79cea13d-6198-45fd-97f5-9e4f9eeb464b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:18:03,946] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:18:03,947] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:18:03,947] [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 09:18:03,949] [INFO] DFAST Taxonomy check result was written to GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 09:18:03,949] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:18:03,949] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:18:03,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79cea13d-6198-45fd-97f5-9e4f9eeb464b/dqc_reference/checkm_data
[2023-06-08 09:18:03,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:18:03,968] [INFO] Task started: CheckM
[2023-06-08 09:18:03,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 09:18:20,747] [INFO] Task succeeded: CheckM
[2023-06-08 09:18:20,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:18:20,761] [INFO] ===== Completeness check finished =====
[2023-06-08 09:18:20,761] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:18:20,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 09:18:20,761] [INFO] Task started: Blastn
[2023-06-08 09:18:20,762] [INFO] Running command: blastn -query GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg79cea13d-6198-45fd-97f5-9e4f9eeb464b/dqc_reference/reference_markers_gtdb.fasta -out GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:18:21,782] [INFO] Task succeeded: Blastn
[2023-06-08 09:18:21,785] [INFO] Selected 13 target genomes.
[2023-06-08 09:18:21,785] [INFO] Target genome list was writen to GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:18:21,789] [INFO] Task started: fastANI
[2023-06-08 09:18:21,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb2a1b94-57dc-4c9d-b737-8018f35b85fc/GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:18:26,113] [INFO] Task succeeded: fastANI
[2023-06-08 09:18:26,124] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:18:26,124] [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_016292445.1	s__F23-B02 sp016292445	95.7881	313	413	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	97.48	96.04	0.83	0.83	3	conclusive
GCA_000431075.1	s__F23-B02 sp000431075	82.8245	324	413	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	97.48	96.66	0.87	0.84	6	-
GCA_003533405.1	s__F23-B02 sp003533405	82.3822	296	413	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	96.88	96.88	0.79	0.79	2	-
GCA_002314685.1	s__F23-B02 sp002314685	79.6267	200	413	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760205.1	s__F23-B02 sp900760205	79.3898	155	413	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.80	98.80	0.91	0.91	2	-
GCA_004558025.1	s__F23-B02 sp004558025	79.2002	185	413	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	99.18	99.18	0.86	0.86	2	-
GCA_001916715.1	s__F23-B02 sp001916715	79.1289	189	413	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.22	97.52	0.91	0.88	7	-
GCA_004557075.1	s__F23-B02 sp004557075	78.9521	178	413	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.03	98.03	0.72	0.72	2	-
GCA_004556755.1	s__F23-B02 sp004556755	78.6358	148	413	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.59	98.13	0.93	0.87	10	-
GCA_900547315.1	s__Limivicinus sp900547315	77.9147	77	413	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.47	98.42	0.88	0.83	3	-
GCA_902775985.1	s__Limivicinus sp902775985	77.1972	53	413	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.70	98.45	0.76	0.73	5	-
GCA_900543625.1	s__CAG-103 sp900543625	77.1397	58	413	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.93	95.23	0.89	0.87	12	-
--------------------------------------------------------------------------------
[2023-06-08 09:18:26,126] [INFO] GTDB search result was written to GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 09:18:26,126] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:18:26,129] [INFO] DFAST_QC result json was written to GCA_945877955.1_ERR1855535_bin.13_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 09:18:26,129] [INFO] DFAST_QC completed!
[2023-06-08 09:18:26,129] [INFO] Total running time: 0h0m35s