[2023-06-19 10:43:00,469] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:43:00,472] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:43:00,472] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfe1e520-d494-457d-98fc-d862e403bd32/dqc_reference
[2023-06-19 10:43:02,571] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:43:02,572] [INFO] Task started: Prodigal
[2023-06-19 10:43:02,572] [INFO] Running command: gunzip -c /var/lib/cwl/stg3104d989-7d6f-43cc-8def-2bbc65a1501d/GCA_018005575.1_ASM1800557v1_genomic.fna.gz | prodigal -d GCA_018005575.1_ASM1800557v1_genomic.fna/cds.fna -a GCA_018005575.1_ASM1800557v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:43:12,101] [INFO] Task succeeded: Prodigal
[2023-06-19 10:43:12,101] [INFO] Task started: HMMsearch
[2023-06-19 10:43:12,102] [INFO] Running command: hmmsearch --tblout GCA_018005575.1_ASM1800557v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfe1e520-d494-457d-98fc-d862e403bd32/dqc_reference/reference_markers.hmm GCA_018005575.1_ASM1800557v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:43:12,335] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:43:12,337] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3104d989-7d6f-43cc-8def-2bbc65a1501d/GCA_018005575.1_ASM1800557v1_genomic.fna.gz]
[2023-06-19 10:43:12,362] [INFO] Query marker FASTA was written to GCA_018005575.1_ASM1800557v1_genomic.fna/markers.fasta
[2023-06-19 10:43:12,363] [INFO] Task started: Blastn
[2023-06-19 10:43:12,363] [INFO] Running command: blastn -query GCA_018005575.1_ASM1800557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfe1e520-d494-457d-98fc-d862e403bd32/dqc_reference/reference_markers.fasta -out GCA_018005575.1_ASM1800557v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:43:12,970] [INFO] Task succeeded: Blastn
[2023-06-19 10:43:12,975] [INFO] Selected 25 target genomes.
[2023-06-19 10:43:12,976] [INFO] Target genome list was writen to GCA_018005575.1_ASM1800557v1_genomic.fna/target_genomes.txt
[2023-06-19 10:43:12,980] [INFO] Task started: fastANI
[2023-06-19 10:43:12,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg3104d989-7d6f-43cc-8def-2bbc65a1501d/GCA_018005575.1_ASM1800557v1_genomic.fna.gz --refList GCA_018005575.1_ASM1800557v1_genomic.fna/target_genomes.txt --output GCA_018005575.1_ASM1800557v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:43:33,212] [INFO] Task succeeded: fastANI
[2023-06-19 10:43:33,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfe1e520-d494-457d-98fc-d862e403bd32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:43:33,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfe1e520-d494-457d-98fc-d862e403bd32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:43:33,215] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:43:33,215] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 10:43:33,216] [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
--------------------------------------------------------------------------------
[2023-06-19 10:43:33,218] [INFO] DFAST Taxonomy check result was written to GCA_018005575.1_ASM1800557v1_genomic.fna/tc_result.tsv
[2023-06-19 10:43:33,218] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:43:33,219] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:43:33,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfe1e520-d494-457d-98fc-d862e403bd32/dqc_reference/checkm_data
[2023-06-19 10:43:33,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:43:33,251] [INFO] Task started: CheckM
[2023-06-19 10:43:33,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018005575.1_ASM1800557v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018005575.1_ASM1800557v1_genomic.fna/checkm_input GCA_018005575.1_ASM1800557v1_genomic.fna/checkm_result
[2023-06-19 10:44:05,445] [INFO] Task succeeded: CheckM
[2023-06-19 10:44:05,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.54%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 10:44:05,469] [INFO] ===== Completeness check finished =====
[2023-06-19 10:44:05,470] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:44:05,470] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018005575.1_ASM1800557v1_genomic.fna/markers.fasta)
[2023-06-19 10:44:05,470] [INFO] Task started: Blastn
[2023-06-19 10:44:05,470] [INFO] Running command: blastn -query GCA_018005575.1_ASM1800557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfe1e520-d494-457d-98fc-d862e403bd32/dqc_reference/reference_markers_gtdb.fasta -out GCA_018005575.1_ASM1800557v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:44:06,353] [INFO] Task succeeded: Blastn
[2023-06-19 10:44:06,358] [INFO] Selected 20 target genomes.
[2023-06-19 10:44:06,359] [INFO] Target genome list was writen to GCA_018005575.1_ASM1800557v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:44:06,373] [INFO] Task started: fastANI
[2023-06-19 10:44:06,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg3104d989-7d6f-43cc-8def-2bbc65a1501d/GCA_018005575.1_ASM1800557v1_genomic.fna.gz --refList GCA_018005575.1_ASM1800557v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018005575.1_ASM1800557v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:44:20,328] [INFO] Task succeeded: fastANI
[2023-06-19 10:44:20,342] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 10:44:20,342] [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_016708765.1	s__JJ008 sp016708765	91.1564	409	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.32	99.14	0.92	0.90	6	-
GCA_016706055.1	s__JJ008 sp016706055	86.6994	385	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.30	99.30	0.94	0.94	2	-
GCA_013140985.1	s__JJ008 sp013140985	79.1111	131	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719165.1	s__JJ008 sp016719165	78.5451	116	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	97.96	97.46	0.92	0.92	3	-
GCA_016719015.1	s__JJ008 sp016719015	78.1224	164	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.23	99.17	0.95	0.92	9	-
GCA_002127295.1	s__JJ008 sp002127295	77.8611	175	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464625.1	s__JJ008 sp001464625	77.5134	165	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786885.1	s__JJ008 sp016786885	76.8496	113	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882315.1	s__VBAR01 sp005882315	76.785	78	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__VBAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331705.1	s__JJ008 sp011331705	76.5468	79	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 10:44:20,360] [INFO] GTDB search result was written to GCA_018005575.1_ASM1800557v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:44:20,361] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:44:20,365] [INFO] DFAST_QC result json was written to GCA_018005575.1_ASM1800557v1_genomic.fna/dqc_result.json
[2023-06-19 10:44:20,365] [INFO] DFAST_QC completed!
[2023-06-19 10:44:20,365] [INFO] Total running time: 0h1m20s